Markers for breast cancer

ABSTRACT

Correlations between polymorphisms and breast cancer are provided. Methods of diagnosing, prognosing, and treating breast cancer are provided. Systems and kits for diagnosis, prognosis and treatment of breast cancer are provided. Methods of identifying breast cancer modulators are also described.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. Ser. No. 12/370,972, filedFeb. 13, 2009, which is a divisional of U.S. Ser. No. 11/606,634, filedNov. 29, 2006, which claims priority to and benefit of U.S. ProvisionalApplication No. 60/740,971, filed Nov. 29, 2005, and also claimspriority to and benefit of U.S. Provisional Application No. 60/781,483,filed Mar. 10, 2006, the contents of each of which are herebyincorporated by reference in their entirety.

BACKGROUND OF THE INVENTION

Breast cancer, like other common cancers, shows familial clustering.Numerous epidemiological studies have demonstrated that, overall, thedisease is approximately twice as common in first degree relatives ofbreast cancer patients¹. Family studies, and particularly twin studies,suggest that most if not all of this clustering has a geneticbasis^(2,3). For example, Peto and Mack³ estimated that the risk ofbreast cancer in the MZ twin of an affected woman was approximatelyfour-fold greater than the risk to a sister of a case.

Several breast cancer susceptibility genes have already been identified,most importantly BRCA1 and BRCA2. Mutations in these genes confer a highrisk of breast cancer (of the order of 65% and 45%, respectively, by age70)⁴. Mutation screening of population-based series of breast cancercases has shown that only about 15% of the familial risk of breastcancer can be explained by mutations in these genes^(5,6). The otherknown breast cancer susceptibility genes (TP53, PTEN, ATM, CHEK2) makeonly small contributions to the familial risk (because the predisposingmutations are rare and/or confer only small risks). In total therefore,the known breast cancer susceptibility genes have been estimated toaccount for no more than 20% of the familial risk⁷.

Genetic variation in risk may result from rare highly-penetrantmutations (such as those in BRCA1 and BRCA2) or from variants conferringmore moderate risks. Several lines evidence suggest strongly that highpenetrance mutations are not major contributors to the residual familialrisk of breast cancer. Firstly, mutation screening of multiple casefamilies has found that the large majority of cases with a very strongfamily history (for example four or more affected relatives) harbormutations in BRCA1 or BRCA2⁸. Secondly, despite extensive efforts overthe past nine years, genetic linkage studies have not identified anyfurther linked loci^(9,10). Thirdly, segregation analyses of largeseries of breast cancer families have found, after adjusting for BRCA1and BRCA2, no evidence for a further major dominant breast cancersusceptibility allele^(11,12). In the largest such analysis, Antoniou etal.¹³ found that the most parsimonious model for breast cancer was apolygenic model, equivalent to a large number of loci of small effectcombining multiplicatively.

While the above analyses suggest, that several low penetrance breastcancer susceptibility genes remain to be detected, the precise number ofsuch genes is unknown. Moreover, in the prior art, it is unclear whethersuch susceptibility alleles are common or rare in the population. Thesubject application focuses on alleles that are relatively common(frequencies greater than 5%) and identification of such loci isperformed herein on a genome-wide basis.

SUMMARY OF THE INVENTION

The invention includes the identification of polymorphic loci that arecorrelated with breast cancer phenotypes, such as susceptibility tobreast cancer. FIGS. 1 and 2 provides descriptions of the phenotypicloci. FIG. 1 provides descriptions of preferred phenotypic loci.Accordingly, this invention provides previously unknown correlationsbetween various polymorphisms and breast cancer susceptibilityphenotypes. The detection of these polymorphisms (or loci linkedthereto), accordingly, provides robust and precise methods and systemsfor identifying patients that are at risk for breast cancer. Inaddition, the identification of these polymorphisms provideshigh-throughput systems and methods for identifying modulators of breastcancer.

Therefore, in one aspect, the invention provides methods of identifyinga breast cancer phenotype for an organism or biological sample derivedtherefrom. The method includes detecting, in the organism or biologicalsample, a polymorphism or a locus closely linked thereto, thepolymorphism being selected from a polymorphism of FIG. 1, wherein thepolymorphism is associated with a breast cancer phenotype. The methodsfurther include correlating the polymorphism or locus to the phenotype.

The organism is typically a mammal, and is preferably a human patient,most typically a human female patient (although breast cancer does occurin men, and the associations noted herein may be applicable to malepatients as well). Similarly, the biological sample is typically derivedfrom a mammal, e.g., a human patient, e.g., following appropriateinformed consent practices. The methods can be used to detect breastcancer markers in samples taken from human patients, or can be used todetect markers in biological samples (e.g., cells, including primary andcultured cells) derived therefrom.

The polymorphisms can be detected by any available method, includingamplification, hybridization to a probe or array, or the like. In onespecific embodiment, Detection includes amplifying the polymorphism,linked locus or a sequence associated therewith (e.g., flankingsequences, transcribed sequences or the like) and detecting theresulting amplicon. For example, in one embodiment, amplifying includesa) admixing an amplification primer or amplification primer pair with anucleic acid template isolated from the organism or biological sample.The primer or primer pair can be complementary or partiallycomplementary to a region proximal to or including the polymorphism orlinked locus, and are capable of initiating nucleic acid polymerizationby a polymerase on the nucleic acid template. The primer or primer pairis extended in a DNA polymerization reaction comprising a polymerase andthe template nucleic acid to generate the amplicon. In certain aspects,the amplicon is optionally detected by a process that includeshybridizing the amplicon to an array, digesting the amplicon with arestriction enzyme, or real-time PCR analysis. Optionally, the ampliconcan be fully or partially sequenced, e.g., by hybridization. Typically,amplification can include performing a polymerase chain reaction (PCR),reverse transcriptase PCR (RT-PCR), or ligase chain reaction (LCR) usingnucleic acid isolated from the organism or biological sample as atemplate in the PCR, RT-PCR, or LCR. Other technologies can besubstituted for amplification, e.g., use of branched DNA (bDNA) probes.

In typical embodiments, the polymorphism or linked locus can include aSNP. Example alleles include those described in FIGS. 1 and/or 2.Relevant polymorphisms can be those, e.g., of FIG. 1 (most preferred) orFIG. 2. Preferred polymorphisms include SNPs selected from the group ofSNPs described by SNP identification numbers consisting of: SNP ID2312116, SNP ID 1622530, SNP ID 3712013, SNP ID 1509710, SNP ID 843029,SNP ID 1990126 (rs13281615), SNP ID 604819, SNP ID 3025734, SNP ID1152499, SNP ID 4415909, SNP ID 1732681, SNP ID 4281579, SNP ID 4454457,SNP ID 2616199, SNP ID1720694, SNP ID 4077723, SNP ID 3711990, SNP ID3337858, SNP ID 4093095, SNP ID 4213825, SNP ID 3488617, SNP ID 3610210,SNP ID 3451239, SNP ID 1582533, SNP ID 3488150, SNP ID 2770052, SNP ID4141351, SNP ID 1335030, SNP ID 2211665, and SNP ID 4538418. Theseidentification numbers are Perlegen SNP identification numbers (PerlegenSciences, Inc. in Mountain View, Calif.), which are publicly availableand can be viewed with considerable associated information atPerlegen.com, by using the company's available genome browser atgenome.perlegen.com/browser/index.html. Wild card characters (e.g., “*”symbols) can be added at the beginning of the SNP_ID to identifypertinent information for all alleles of the SNP, e.g., following thecomplete instructions provided. This database also links to the NCBIgenomic database, thereby providing considerable additional informationfor the relevant genes and polymorphisms. These SNPs include SNPsassociated with, e.g., the following genes: FGFR2, A2BP1, TNRC9, H19,FSTL5, LSP1, LOC388927, UNQ9391, HCN1, LOC441192, TNRC9, NR3C2,KIAA0826, FLJ31033, AACS, FRMD4A and SEC31L2 (See also, FIG. 1).Polymorphisms linked to these genes are, accordingly, also preferredSNPs that can be associated with breast cancer polymorphisms.

Optionally, and, in certain embodiments, preferably, the method includesdetecting polymorphisms in more than one such gene (e.g., in certainconvenient applications, several polymorphisms can be detectedsimultaneously for a single patient to more completely determine orassign the relevant phenotype). Thus, in one aspect, the inventionincludes detecting a plurality of polymorphisms or linked loci in aplurality of said genes. This can include, e.g., detecting at least onepolymorphism for each of: SNP ID 2312116, SNP ID 1622530, SNP ID3712013, SNP ID 1509710 and SNP ID 84302, and/or polymorphism in FGFR2,A2BP1, TNRC9, H19, and FSTL5. Similarly, the method can includedetecting at least one polymorphism for each of: SNP ID 2312116, SNP ID1622530, SNP ID 3712013, SNP ID 1509710, SNP ID 843029, SNP ID 1990126,SNP ID 604819, SNP ID 3025734, SNP ID 1152499, SNP ID 4415909, SNP ID1732681, SNP ID 4281579, SNP ID 4454457, SNP ID 2616199, SNP ID 1720694,SNP ID 4077723, SNP ID 3711990, SNP ID 3337858, SNP ID 4093095, SNP ID4213825, SNP ID 3488617, SNP ID 3610210, SNP ID 3451239, SNP ID 1582533,SNP ID 3488150, SNP ID 2770052, SNP ID 4141351, SNP ID 1335030, SNP ID2211665, and SNP ID 4538418, or at least one polymorphism in each of:FGFR2, A2BP1, TNRC9, H19, FSTL5, LSP1, LOC388927, UNQ9391, HCN1,LOC441192, TNRC9, NR3C2, KIAA0826, FLJ31033, AACS, FRMD4A and SEC31L2.In general, any combination of these or any otherpolymorphism/gene/locus in the figures herein can be detected, and allsuch combinations are optionally a feature of the invention, whetherlisted expressly or not. Probes or primers of the invention useful indetecting the polymorphisms herein can include a nucleotide sequence ofa polymorphism of FIGS. 1 and/or 2, a flanking sequence thereof, or acomplementary nucleic acid thereof, or a transcribed product thereof(e.g., a nRNA or mRNA form produced from a genomic sequence, e.g., bytranscription or splicing). Polymorphisms can also be detected in apolypeptide sequence, e.g., for any polypeptide sequence transcribedfrom a given allelic form of a nucleic acid.

In general, any polymorphism that is linked to a QTL can be used as amarker for the QTL. Thus, markers linked to a given polymorphism of theFigures can be used as proxy markers for the given polymorphism. Ingeneral, the closer the linkage, the better the marker will be for aQTL/polymorphism. Thus, desirably, the linked locus can be a closelylinked locus that is about 5 cM or less (and, optionally, 1 cM or less)from the polymorphism.

The methods optionally include correlating the polymorphism or linkedlocus to the breast cancer phenotype by referencing a look up table thatcomprises correlation information for alleles of the polymorphism orlinked locus and the breast cancer phenotype. Databases that are usedfor this correlation can be heuristic, or otherwise capable of refiningcorrelations based on information obtained by correlating marker-traitinformation.

Related compositions are a feature of the invention, e.g., a compositioncomprising a plurality of marker probes or amplification primers thatdetect or amplify a plurality of polymorphisms associated with a breastcancer phenotype, e.g., as described herein. The primers/probes can bearray based, or free in solution.

In an additional aspect, methods of identifying a modulator of a breastcancer phenotype are also provided. The methods include contacting apotential modulator to a gene or gene product, e.g., wherein the gene orgene product comprises or is closely linked to a polymorphism describedherein (e.g., in FIGS. 1 and/or 2). An effect of the potential modulatoron the gene or gene product is detected, thereby identifying whether thepotential modulator modulates the phenotype.

The gene or gene product optionally includes a particular allele of apolymorphism selected from those listed herein, but modulators can alsobe tested on other alleles to identify modulators that modulate allelesspecifically or non-specifically. The effects that can be tested forinclude any of: (a) increased or decreased expression of the gene orgene product in the presence of the modulator; (b) increased ordecreased activity of the gene product in the presence of the modulator;and, (c) an altered expression pattern of the gene or gene product inthe presence of the modulator.

A kit for treatment of a breast cancer phenotype can include a modulatoridentified by the method and instructions for administering themodulator to a patient to treat the phenotype.

In addition to the methods noted above, kits and systems for practicingthe methods are also a feature of the invention. For example, a systemfor identifying a breast cancer phenotype for an organism or biologicalsample derived therefrom are one feature of the invention. The systemincludes, e.g., a set of marker probes or primers configured to detectat least one allele of one or more polymorphism or linked locus, e.g.,where the polymorphism is any polymorphism noted herein, e.g., in FIGS.1 or 2. The system optionally additionally includes a detector that isconfigured to detect one or more signal outputs from the set of markerprobes or primers, or an amplicon produced from the set of marker probesor primers, thereby identifying the presence or absence of the allele.System instructions (e.g., software embodied in a computer of thesystem) that correlate the presence or absence of the allele with apredicted phenotype are typically included as components of the system.

Systems for screening modulators are also a feature of the invention.The systems can include, e.g., genes linked to a polymorphism herein, oran encoded expression products of the gene. The systems will typicallyinclude a detector that measures increased or decreased expression ofthe gene or gene product in the presence of the modulator; increased ordecreased activity of the gene product in the presence of the modulator;or an altered expression pattern of the gene or gene product in thepresence of the modulator. The systems can also include fluid handlingelements for mixing and aliquotting modulator and/or the gene orproduct, mixing them, performing laboratory operations (e.g.,purification, synthesis, cell culture, etc.). System instructions forrecording modulator effects and, optionally, for selecting modulatorsare also an optional feature of these systems.

Kits for performing any of the methods herein are another feature of theinvention. Such kits can include probes or amplicons for detecting anypolymorphism herein, appropriate packaging materials, and instructionsfor practicing the methods.

The polymorphisms and genes, and corresponding marker probes, ampliconsor primers described above can be embodied in any system herein, eitherin the form of physical nucleic acids or polypeptides, or in the form ofsystem instructions that include sequence information for the nucleicacids and polypeptides. For example, the system can include primers oramplicons corresponding to (or that amplify a portion of) a gene orpolymorphism described herein, such as SNP ID 2312116, SNP ID 1622530,SNP ID 3712013, SNP ID 1509710, SNP ID 843029, SNP ID 1990126, SNP ID604819, SNP ID 3025734, SNP ID 1152499, SNP ID 4415909, SNP ID 1732681,SNP ID 4281579, SNP ID 4454457, SNP ID 2616199, SNP ID 1720694, SNP ID4077723, SNP ID 3711990, SNP ID 3337858, SNP ID 4093095, SNP ID 4213825,SNP ID 3488617, SNP ID 3610210, SNP ID 3451239, SNP ID 1582533, SNP ID3488150, SNP ID 2770052, SNP ID 4141351, SNP ID 1335030, SNP ID 2211665,and SNP ID 4538418, and/or FGFR2, A2BP1, TNRC9, H19, FSTL5, LSP1,LOC388927, UNQ9391, HCN1, LOC441192, TNRC9, NR3C2, KIAA0826, FLJ31033,AACS, FRMD4A and SEC31L2. As in the methods above, the set of markerprobes or primers optionally detects a plurality of polymorphisms in aplurality of said genes or genetic loci. Thus, for example, the set ofmarker probes or primers detects at least one polymorphism in each ofthese polymorphisms or genes, or any other polymorphism, gene or locusin the Figures herein. Any such probe or primer can include a nucleotidesequence of any such polymorphism or gene, or a complementary nucleicacid thereof, or a transcribed product thereof (e.g., a nRNA or mRNAform produced from a genomic sequence, e.g., by transcription orsplicing).

Many alternate variants are embodiments of the invention. For example,the detector typically detects one or more light emission that isindicative of the presence or absence of the allele. The instructionstypically comprise at least one look-up table that includes acorrelation between the presence or absence of the allele and thephenotype. The system optionally comprises a sample for testing, e.g., agenomic DNA, amplified genomic DNA, cDNA, amplified cDNA, RNA, oramplified RNA. The sample can be from or derived from a mammal such as ahuman patient.

All features of the methods, kits and systems can be used together incombination. For example, systems for detecting modulators can be usedfor practicing methods of modulator detection. Systems for identifyingcorrelations between breast cancer phenotypes and polymorphisms can beused for practicing the methods herein. Kits can be used for practicingthe methods herein. Thus, described features of the systems, methods andkits can be applied to the different systems, methods and kits herein.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 is a table of preferred polymorphisms, genes and relatedinformation for polymorphisms associated with breast cancer.

FIG. 2 is a table of preferred polymorphisms, genes and relatedinformation for polymorphisms associated with breast cancer.

DEFINITIONS

It is to be understood that this invention is not limited to particularembodiments, which can, of course, vary. It is also to be understoodthat the terminology used herein is for the purpose of describingparticular embodiments only, and is not intended to be limiting. As usedin this specification and the appended claims, terms in the singular andthe singular forms “a,” “an” and “the,” for example, optionally includeplural referents unless the content clearly dictates otherwise. Thus,for example, reference to “a probe” optionally includes a plurality ofprobe molecules; similarly, depending on the context, use of the term “anucleic acid” optionally includes, as a practical matter, many copies ofthat nucleic acid molecule. Letter designations for genes or proteinscan refer to the gene form and/or the protein form, depending oncontext. One of skill is fully able to relate the nucleic acid and aminoacid forms of the relevant biological molecules by reference to thesequences herein, known sequences and the genetic code.

Unless otherwise indicated, nucleic acids are written left to right in a5′ to 3′ orientation. Numeric ranges recited within the specificationare inclusive of the numbers defining the range and include each integeror any non-integer fraction within the defined range. Unless definedotherwise, all technical and scientific terms used herein have the samemeaning as commonly understood by one of ordinary skill in the art towhich the invention pertains. Although any methods and materials similaror equivalent to those described herein can be used in the practice fortesting of the present invention, the preferred materials and methodsare described herein. In describing and claiming the present invention,the following terminology will be used in accordance with thedefinitions set out below.

A “phenotype” is a trait or collection of traits that is/are observablein an individual or population. The trait can be quantitative (aquantitative trait, or QTL) or qualitative. For example, susceptibilityto breast cancer is a phenotype that can be monitored according to themethods, compositions, kits and systems herein.

A “breast cancer susceptibility phenotype” is a phenotype that displaysa predisposition towards developing breast cancer in an individual. Aphenotype that displays a predisposition for breast cancer, can, forexample, show a higher likelihood that the cancer will develop in anindividual with the phenotype than in members of a relevant generalpopulation under a given set of environmental conditions (diet, physicalactivity regime, geographic location, etc.).

A “polymorphism” is a locus that is variable; that is, within apopulation, the nucleotide sequence at a polymorphism has more than oneversion or allele. The term “allele” refers to one of two or moredifferent nucleotide sequences that occur or are encoded at a specificlocus, or two or more different polypeptide sequences encoded by such alocus. For example, a first allele can occur on one chromosome, while asecond allele occurs on a second homologous chromosome, e.g., as occursfor different chromosomes of a heterozygous individual, or betweendifferent homozygous or heterozygous individuals in a population. Oneexample of a polymorphism is a “single nucleotide polymorphism” (SNP),which is a polymorphism at a single nucleotide position in a genome (thenucleotide at the specified position varies between individuals orpopulations).

An allele “positively” correlates with a trait when it is linked to itand when presence of the allele is an indictor that the trait or traitform will occur in an individual comprising the allele. An allelenegatively correlates with a trait when it is linked to it and whenpresence of the allele is an indicator that a trait or trait form willnot occur in an individual comprising the allele.

A marker polymorphism or allele is “correlated” or “associated” with aspecified phenotype (breast cancer susceptibility, etc.) when it can bestatistically linked (positively or negatively) to the phenotype. Thatis, the specified polymorphism occurs more commonly in a case population(e.g., breast cancer patients) than in a control population (e.g.,individuals that do not have breast cancer). This correlation is ofteninferred as being causal in nature, but it need not be-simple geneticlinkage to (association with) a locus for a trait that underlies thephenotype is sufficient for correlation/association to occur.

A “favorable allele” is an allele at a particular locus that positivelycorrelates with a desirable phenotype, e.g., resistance to breastcancer, e.g., an allele that negatively correlates with predispositionto breast cancer. A favorable allele of a linked marker is a markerallele that segregates with the favorable allele. A favorable allelicform of a chromosome segment is a chromosome segment that includes anucleotide sequence that positively correlates with the desiredphenotype, or that negatively correlates with the unfavorable phenotypeat one or more genetic loci physically located on the chromosomesegment.

An “unfavorable allele” is an allele at a particular locus thatnegatively correlates with a desirable phenotype, or that correlatespositively with an undesirable phenotype, e.g., positive correlation tobreast cancer susceptibility. An unfavorable allele of a linked markeris a marker allele that segregates with the unfavorable allele. Anunfavorable allelic form of a chromosome segment is a chromosome segmentthat includes a nucleotide sequence that negatively correlates with thedesired phenotype, or positively correlates with the undesirablephenotype at one or more genetic loci physically located on thechromosome segment.

“Allele frequency” refers to the frequency (proportion or percentage) atwhich an allele is present at a locus within an individual, within aline, or within a population of lines. For example, for an allele “A,”diploid individuals of genotype “AA, “Aa,” or “aa” have allelefrequencies of 1.0, 0.5, or 0.0, respectively. One can estimate theallele frequency within a line or population (e.g., cases or controls)by averaging the allele frequencies of a sample of individuals from thatline or population. Similarly, one can calculate the allele frequencywithin a population of lines by averaging the allele frequencies oflines that make up the population.

An individual is “homozygous” if the individual has only one type ofallele at a given locus (e.g., a diploid individual has a copy of thesame allele at a locus for each of two homologous chromosomes). Anindividual is “heterozygous” if more than one allele type is present ata given locus (e.g., a diploid individual with one copy each of twodifferent alleles). The term “homogeneity” indicates that members of agroup have the same genotype at one or more specific loci. In contrast,the term “heterogeneity” is used to indicate that individuals within thegroup differ in genotype at one or more specific loci.

A “locus” is a chromosomal position or region. For example, apolymorphic locus is a position or region where a polymorphic nucleicacid, trait determinant, gene or marker is located. In a furtherexample, a “gene locus” is a specific chromosome location (region) inthe genome of a species where a specific gene can be found. Similarly,the term “quantitative trait locus” or “QTL” refers to a locus with atleast two alleles that differentially affect the expression or alter thevariation of a quantitative or continuous phenotypic trait in at leastone genetic background, e.g., in at least one population or progeny.

A “marker,” “molecular marker” or “marker nucleic acid” refers to anucleotide sequence or encoded product thereof (e.g., a protein) used asa point of reference when identifying a locus or a linked locus. Amarker can be derived from genomic nucleotide sequence or from expressednucleotide sequences (e.g., from an RNA, nRNA, mRNA, a cDNA, etc.), orfrom an encoded polypeptide. The term also refers to nucleic acidsequences complementary to or flanking the marker sequences, such asnucleic acids used as probes or primer pairs capable of amplifying themarker sequence. A “marker probe” is a nucleic acid sequence or moleculethat can be used to identify the presence of a marker locus, e.g., anucleic acid probe that is complementary to a marker locus sequence.Nucleic acids are “complementary” when they specifically hybridize insolution, e.g., according to Watson-Crick base pairing rules. A “markerlocus” is a locus that can be used to track the presence of a secondlinked locus, e.g., a linked or correlated locus that encodes orcontributes to the population variation of a phenotypic trait. Forexample, a marker locus can be used to monitor segregation of alleles ata locus, such as a QTL, that are genetically or physically linked to themarker locus. Thus, a “marker allele,” alternatively an “allele of amarker locus” is one of a plurality of polymorphic nucleotide sequencesfound at a marker locus in a population that is polymorphic for themarker locus. In one aspect, the present invention provides marker locicorrelating with a phenotype of interest, e.g., breast cancersusceptibility/resistance. Each of the identified markers is expected tobe in close physical and genetic proximity (resulting in physical and/orgenetic linkage) to a genetic element, e.g., a QTL, that contributes tothe relevant phenotype. Markers corresponding to genetic polymorphismsbetween members of a population can be detected by methodswell-established in the art. These include, e.g., PCR-based sequencespecific amplification methods, detection of restriction fragment lengthpolymorphisms (RFLP), detection of isozyme markers, detection of allelespecific hybridization (ASH), detection of single nucleotide extension,detection of amplified variable sequences of the genome, detection ofself-sustained sequence replication, detection of simple sequencerepeats (SSRs), detection of single nucleotide polymorphisms (SNPs), ordetection of amplified fragment length polymorphisms (AFLPs).

A “genetic map” is a description of genetic linkage (or association)relationships among loci on one or more chromosomes (or linkage groups)within a given species, generally depicted in a diagrammatic or tabularform. “Mapping” is the process of defining the linkage relationships ofloci through the use of genetic markers, populations segregating for themarkers, and standard genetic principles of recombination frequency. A“map location” is an assigned location on a genetic map relative tolinked genetic markers where a specified marker can be found within agiven species. The term “chromosome segment” or designates a contiguouslinear span of genomic DNA that resides on a single chromosome.Similarly, a “haplotype” is a set of genetic loci found in the heritablematerial of an individual or population (the set can be a contiguous ornon-contiguous). In the context of the present invention geneticelements such as one or more alleles herein and one or more linkedmarker alleles can be located within a chromosome segment and are also,accordingly, genetically linked, a specified genetic recombinationdistance of less than or equal to 20 centimorgan (cM) or less, e.g., 15cM or less, often 10 cM or less, e.g., about 9, 8, 7, 6, 5, 4, 3, 2, 1,0.75, 0.5, 0.25, or 0.1 CM or less. That is, two closely linked geneticelements within a single chromosome segment undergo recombination duringmeiosis with each other at a frequency of less than or equal to about20%, e.g., about 19%, 18%, 17%, 16%, 15%, 14%, 13%, 12%, 11%, 10%, 9%,8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, 0.75%, 0.5%, 0.25%, or 0.1% or less.Once a correlation/association between a phenotype (e.g., breast cancerpredisposition) and a polymorphic locus in identified, e.g., bycomparison of a statistical frequency of the locus in cases andcontrols, any polymorphism that is linked to the associated locus can beused as a proxy marker for the correlated locus.

A “genetic recombination frequency” is the frequency of a recombinationevent between two genetic loci. Recombination frequency can be observedby following the segregation of markers and/or traits during meiosis. Inthe context of this invention, a marker locus is “associated with”another marker locus or some other locus (for example, a breast cancersusceptibility locus), when the relevant loci are part of the samelinkage group, due to physical chromosomal association, and are inlinkage disequilibrium. This occurs when the marker locus and a linkedlocus are found together in progeny more frequently than if the locisegregate randomly. Similarly, a marker locus can also be associatedwith a trait, e.g., a marker locus can be “associated with” a giventrait (breast cancer resistance or susceptibility) when the marker locusis in linkage disequilibrium with the trait (this can be detected, e.g.,when the marker is found more commonly in case versus controlpopulations). The term “linkage disequilibrium” refers to a non-randomsegregation of genetic loci or traits (or both). In either case, linkagedisequilibrium implies that the relevant loci are within sufficientphysical proximity along a length of a chromosome so that they segregatetogether with greater than random frequency (in the case ofco-segregating traits, the loci that underlie the traits are insufficient proximity to each other). Linked loci co-segregate more than50% of the time, e.g., from about 51% to about 100% of the time.Advantageously, the two loci are located in close proximity such thatrecombination between homologous chromosome pairs does not occur betweenthe two loci during meiosis with high frequency, e.g., such that closelylinked loci co-segregate at least about 80% of the time, more preferablyat least about 85% of the time, still more preferably at least 90% ofthe time, e.g., 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5%,99.75%, or 99.90% or more of the time.

The phrase “closely linked,” in the present application, means thatrecombination between two linked loci (e.g., a SNP such as oneidentified in FIGS. 1 or 2 (e.g., that is correlated to a breast cancerphenotype by comparison of case and control populations) and a secondlinked polymorphism) occurs with a frequency of equal to or less thanabout 20%. Put another way, the closely (or “tightly”) linked locico-segregate at least 80% of the time. Marker loci are especially usefulin the present invention when they are closely linked to target loci(e.g., QTL for breast cancer, or, alternatively, simply other breastcancer marker loci). The more closely a marker is linked to a targetlocus, the better an indicator for the target locus that the marker is.Thus, in one embodiment, tightly linked loci such as a marker locus anda second locus display an inter-locus recombination frequency of about20% or less, e.g., 15% or less, e.g., 10% or less, preferably about 9%or less, still more preferably about 8% or less, yet more preferablyabout 7% or less, still more preferably about 6% or less, yet morepreferably about 5% or less, still more preferably about 4% or less, yetmore preferably about 3% or less, and still more preferably about 2% orless. In highly preferred embodiments, the relevant loci (e.g., a markerlocus and a target locus such as a QTL) display a recombinationfrequency of about 1% or less, e.g., about 0.75% or less, morepreferably about 0.5% or less, or yet more preferably about 0.25% orless, or still more preferably about 0.1% or less. Two loci that arelocalized to the same chromosome, and at such a distance thatrecombination between the two loci occurs at a frequency of less thanabout 20%, e.g., 15%, more preferably 10% (e.g., about 9%, 8%, 7%, 6%,5%, 4%, 3%, 2%, 1%, 0.75%, 0.5%, 0.25%, 0.1% or less) are also said tobe “proximal to” each other. When referring to the relationship betweentwo linked genetic elements, such as a genetic element contributing to atrait and a proximal marker, “coupling” phase linkage indicates thestate where the “favorable” allele at the trait locus is physicallyassociated on the same chromosome strand as the “favorable” allele ofthe respective linked marker locus. In coupling phase, both favorablealleles are inherited together by progeny that inherit that chromosomestrand. In “repulsion” phase linkage, the “favorable” allele at thelocus of interest (e.g., a QTL for breast cancer susceptibility) isphysically associated on the same chromosome strand as an “unfavorable”allele at the proximal marker locus, and the two “favorable” alleles arenot inherited together (i.e., the two loci are “out of phase” with eachother).

The term “amplifying” in the context of nucleic acid amplification isany process whereby additional copies of a selected nucleic acid (or atranscribed form thereof) are produced. Typical amplification methodsinclude various polymerase based replication methods, including thepolymerase chain reaction (PCR), ligase mediated methods such as theligase chain reaction (LCR) and RNA polymerase based amplification(e.g., by transcription) methods. An “amplicon” is an amplified nucleicacid, e.g., a nucleic acid that is produced by amplifying a templatenucleic acid by any available amplification method (e.g., PCR, LCR,transcription, or the like).

A “genomic nucleic acid” is a nucleic acid that corresponds in sequenceto a heritable nucleic acid in a cell. Common examples include nucleargenomic DNA and amplicons thereof. A genomic nucleic acid is, in somecases, different from a spliced RNA, or a corresponding cDNA, in thatthe spliced RNA or cDNA is processed, e.g., by the splicing machinery,to remove introns. Genomic nucleic acids optionally comprisenontranscribed (e.g., chromosome structural sequences, promoter regions,enhancer regions, etc.) and/or non-translated sequences (e.g., introns),whereas spliced RNA/cDNA typically do not have introns. A “templategenomic nucleic acid” is a genomic nucleic acid that serves as atemplate in an amplification reaction (e.g., a polymerase basedamplification reaction such as PCR, a ligase mediated amplificationreaction such as LCR, a transcription reaction, or the like).

An “exogenous nucleic acid” is a nucleic acid that is not native to aspecified system (e.g., a germplasm, cell, individual, etc.), withrespect to sequence, genomic position, or both. As used herein, theterms “exogenous” or “heterologous” as applied to polynucleotides orpolypeptides typically refers to molecules that have been artificiallysupplied to a biological system (e.g., a cell, an individual, etc.) andare not native to that particular biological system. The terms canindicate that the relevant material originated from a source other thana naturally occurring source, or can refer to molecules having anon-natural configuration, genetic location or arrangement of parts.

The term “introduced” when referring to translocating a heterologous orexogenous nucleic acid into a cell refers to the incorporation of thenucleic acid into the cell using any methodology. The term encompassessuch nucleic acid introduction methods as “transfection,”“transformation” and “transduction.”

As used herein, the term “vector” is used in reference topolynucleotides or other molecules that transfer nucleic acid segment(s)into a cell. The term “vehicle” is sometimes used interchangeably with“vector.” A vector optionally comprises parts which mediate vectormaintenance and enable its intended use (e.g., sequences necessary forreplication, genes imparting drug or antibiotic resistance, a multiplecloning site, operably linked promoter/enhancer elements which enablethe expression of a cloned gene, etc.). Vectors are often derived fromplasmids, bacteriophages, or plant or animal viruses. A “cloning vector”or “shuttle vector” or “subcloning vector” contains operably linkedparts that facilitate subcloning steps (e.g., a multiple cloning sitecontaining multiple restriction endonuclease sites).

The term “expression vector” as used herein refers to a vectorcomprising operably linked polynucleotide sequences that facilitateexpression of a coding sequence in a particular host organism (e.g., abacterial expression vector or a mammalian cell expression vector).Polynucleotide sequences that facilitate expression in prokaryotestypically include, e.g., a promoter, an operator (optional), and aribosome binding site, often along with other sequences. Eukaryoticcells can use promoters, enhancers, termination and polyadenylationsignals and other sequences that are generally different from those usedby prokaryotes. In one optional embodiment, a gene corresponding to aloci herein is cloned into an expression vector and expressed, with thegene product(s) to be used in the methods and systems herein formodulator identification.

A specified nucleic acid is “derived from” a given nucleic acid when itis constructed using the given nucleic acid's sequence, or when thespecified nucleic acid is constructed using the given nucleic acid.

A “gene” is one or more sequence(s) of nucleotides in a genome thattogether encode one or more expressed molecule, e.g., an RNA, orpolypeptide. The gene can include coding sequences that are transcribedinto RNA which may then be translated into a polypeptide sequence, andcan include associated structural or regulatory sequences that aid inreplication or expression of the gene. Genes of interest in the presentinvention include those that include or are closely linked to the lociof FIGS. 1 and/or 2.

A “genotype” is the genetic constitution of an individual (or group ofindividuals) at one or more genetic loci. Genotype is defined by theallele(s) of one or more known loci of the individual, typically, thecompilation of alleles inherited from its parents. A “haplotype” is thegenotype of an individual at a plurality of genetic loci on a single DNAstrand. Typically, the genetic loci described by a haplotype arephysically and genetically linked, i.e., on the same chromosome strand.

A “set” of markers or probes refers to a collection or group of markersor probes, or the data derived therefrom, used for a common purpose,e.g., identifying an individual with a specified phenotype (e.g., breastcancer resistance or susceptibility). Frequently, data corresponding tothe markers or probes, or derived from their use, is stored in anelectronic medium. While each of the members of a set possess utilitywith respect to the specified purpose, individual markers selected fromthe set as well as subsets including some, but not all of the markers,are also effective in achieving the specified purpose.

A “look up table” is a table that correlates one form of data toanother, or one or more forms of data with a predicted outcome to whichthe data is relevant. For example, a look up table can include acorrelation between allele data and a predicted trait that an individualcomprising one or more given alleles is likely to display. These tablescan be, and typically are, multidimensional, e.g., taking multiplealleles into account simultaneously, and, optionally, taking otherfactors into account as well, such as genetic background, e.g., inmaking a trait prediction.

A “computer readable medium” is an information storage media that can beaccessed by a computer using an available or custom interface. Examplesinclude memory (e.g., ROM or RAM, flash memory, etc.), optical storagemedia (e.g., CD-ROM), magnetic storage media (computer hard drives,floppy disks, etc.), punch cards, and many others that are commerciallyavailable. Information can be transmitted between a system of interestand the computer, or to or from the computer to or from the computerreadable medium for storage or access of stored information. Thistransmission can be an electrical transmission, or can be made by otheravailable methods, such as an IR link, a wireless correction, or thelike.

“System instructions” are instruction sets that can be partially orfully executed by the system. Typically, the instruction sets arepresent as system software.

A “translation product” is a product (typically a polypeptide) producedas a result of the translation of a nucleic acid. A “transcriptionproduct” is a product (e.g., an RNA, optionally including mRNA, or,e.g., a catalytic or biologically active RNA) produced as a result oftranscription of a nucleic acid (e.g., a DNA).

An “array” is an assemblage of elements. The assemblage can be spatiallyordered (a “patterned array”) or disordered (a “randomly patterned”array). The array can form or comprise one or more functional elements(e.g., a probe region on a microarray) or it can be non-functional.

As used herein, the term “SNP” or “single nucleotide polymorphism”refers to a genetic variation between individuals; e.g., a singlenitrogenous base position in the DNA of organisms that is variable. Asused herein, “SNPs” is the plural of SNP. Of course, when one refers toDNA herein, such reference may include derivatives of the DNA such asamplicons, RNA transcripts thereof, etc.

DETAILED DESCRIPTION Overview

The invention includes new correlations between the polymorphisms ofFIGS. 1 and 2 (and genes that include or are proximal to thepolymorphisms) and breast cancer predisposition. Certain alleles in, andlinked to, these genes or gene products are predictive of the likelihoodthat an individual possessing the relevant alleles will develop breastcancer. Accordingly, detection of these alleles, by any availablemethod, can be used for diagnostic purposes such as early detection ofsusceptibility to breast cancer, prognosis for patients that presentwith breast cancer and in assisting in diagnosis, e.g., where currentcriteria are insufficient for a definitive diagnosis.

The identification that the polymorphisms, genes or gene products ofFIGS. 1 or 2, are correlated with breast cancer phenotypes also providesa platform for screening potential modulators of breast cancerdisorders. Modulators of the activity of any genes or encoded proteinscorresponding to the polymorphisms of FIGS. 1 and 2, are expected tohave an effect on breast cancer. Thus, methods of screening, systems forscreening and the like, are features of the invention. Modulatorsidentified by these screening approaches are also a feature of theinvention.

Kits for the diagnosis and treatment of breast cancer, e.g., comprisingprobes to identify relevant alleles, packaging materials, andinstructions for con-elating detection of relevant alleles to breastcancer are also a feature of the invention. These kits can also includemodulators of breast cancer and/or instructions for treating patientsusing conventional methods.

Methods of Identifying Breast Cancer Predisposition

As noted, the invention provides the discovery that certain genes orother loci of FIGS. 1 and 2, are linked to breast cancer phenotypes.Thus, by detecting markers (e.g., the SNPs in FIGS. 1 or 2 or lociclosely linked thereto) that con-elate, positively or negatively, withthe relevant phenotypes, it can be determined whether an individual orpopulation is likely to be comprise these phenotypes. This providesenhanced early detection options to identify patients that are at riskfor breast cancer, making it possible, in some cases, to prevent actualdevelopment of cancer, e.g., by taking early preventative action (e.g.,any existing therapy, including prophylactic surgery, diet, exercise,available medications, etc.). In addition, use of the various markersherein also adds certainty to existing diagnostic techniques foridentifying whether a patient is suffering from a particular form ofbreast cancer. Furthermore, knowledge of whether there is a molecularbasis for the disease can also assist in determining patient prognosis,e.g., by providing an indication of how likely it is that a patient canrespond to conventional therapy for breast cancer. Disease treatment canalso be targeted based on what type of molecular disorder the patientdisplays.

Detection methods for detecting relevant alleles can include anyavailable method, e.g., amplification technologies. For example,detection can include amplifying the polymorphism or a sequenceassociated therewith and detecting the resulting amplicon. This caninclude admixing an amplification primer or amplification primer pairwith a nucleic acid template isolated from the organism or biologicalsample (e.g., comprising the SNP or other polymorphism), e.g., where theprimer or primer pair is complementary or partially complementary to atleast a portion of the gene or tightly linked polymorphism, or to asequence proximal thereto. The primer is typically capable of initiatingnucleic acid polymerization by a polymerase on the nucleic acidtemplate. The primer or primer pair is extended, e.g., in a DNApolymerization reaction (PCR, RT-PCR, etc.) comprising a polymerase andthe template nucleic acid to generate the amplicon. The amplicon isdetected by any available detection process, e.g., sequencing,hybridizing the amplicon to an array (or affixing the amplicon to anarray and hybridizing probes to it), digesting the amplicon with arestriction enzyme (e.g., RFLP), real-time PCR analysis, singlenucleotide extension, allele-specific hybridization, or the like.

The correlation between a detected polymorphism and a trait can beperformed by any method that can identify a relationship between anallele and a phenotype. Most typically, these methods involvereferencing a look up table that comprises correlations between allelesof the polymorphism and the phenotype. The table can include data formultiple allele-phenotype relationships and can take account of additiveor other higher order effects of multiple allele-phenotyperelationships, e.g., through the use of statistical tools such asprinciple component analysis, heuristic algorithms, etc.

Within the context of these methods, the following discussion firstfocuses on how markers and alleles are linked and how this phenomenoncan be used in the context of methods for identifying breast cancerphenotypes, and then focuses on marker detection methods. Additionalsections below discuss data analysis.

Markers, Linkage and Alleles

In traditional linkage (or association) analysis, no direct knowledge ofthe physical relationship of genes on a chromosome is required. Mendel'sfirst law is that factors of pairs of characters are segregated, meaningthat alleles of a diploid trait separate into two gametes and then intodifferent offspring. Classical linkage analysis can be thought of as astatistical description of the relative frequencies of cosegregation ofdifferent traits. Linkage analysis is the well characterized descriptiveframework of how traits are grouped together based upon the frequencywith which they segregate together. That is, if two non-allelic traitsare inherited together with a greater than random frequency, they aresaid to be “linked.” The frequency with which the traits are inheritedtogether is the primary measure of how tightly the traits are linked,i.e., traits which are inherited together with a higher: frequency aremore closely linked than traits which are inherited together with lower(but still above random) frequency. Traits are linked because the geneswhich underlie the traits reside near one another on the samechromosome. The further apart on a chromosome the genes reside, the lesslikely they are to segregate together, because homologous chromosomesrecombine during meiosis. Thus, the further apart on a chromosome thegenes reside, the more likely it is that there will be a recombinationevent during meiosis that will result in two genes segregatingseparately into progeny.

A common measure of linkage (or association) is the frequency with whichtraits cosegregate. This can be expressed as a percentage ofcosegregation (recombination frequency) or, also commonly, incentiMorgans (cM), which are actually a reciprocal unit of recombinationfrequency. The cM is named after the pioneering geneticist Thomas HuntMorgan and is a unit of measure of genetic recombination frequency. OnecM is equal to a 1% chance that a trait at one genetic locus will beseparated from a trait at another locus due to recombination in a singlegeneration (meaning the traits segregate together 99% of the time).Because chromosomal distance is approximately proportional to thefrequency of recombination events between traits, there is anapproximate physical distance that correlates with recombinationfrequency. For example, in humans, 1 cM correlates, on average, to about1 million base pairs (1 Mbp).

Marker loci are themselves traits and can be assessed according tostandard linkage analysis by tracking the marker loci duringsegregation. Thus, in the context of the present invention, one cM isequal to a 1% chance that a marker locus will be separated from anotherlocus (which can be any other trait, e.g., another marker locus, oranother trait locus that encodes a QTL for breast cancer), due torecombination in a single generation. The markers herein, e.g., thoselisted in FIGS. 1 and 2, can correlate with breast cancer. This meansthat the markers comprise or are sufficiently proximal to a QTL forbreast cancer that they can be used as a predictor for the trait itself.This is extremely useful in the context of disease diagnosis.

The polymorphisms of FIGS. 1 and 2 have been identified as being moreprevalent in case (breast cancer patient) versus control populations.Any marker that is linked to a trait locus of interest (e.g., in thepresent case, a QTL or identified linked marker locus for breast cancer,e.g., as in FIGS. 1 and 2) can be used as a marker for that trait. Thus,in addition to the markers noted in FIGS. 1 and 2, other markers closelylinked to the markers itemized in these Figures can also usefullypredict the presence of the marker alleles indicated in the figures(and, thus, the relevant phenotypic trait). Such linked markers areparticularly useful when they are sufficiently proximal to a given locusso that they display a low recombination frequency with the given locus.In the present invention, such closely linked markers are a feature ofthe invention. Closely linked loci display a recombination frequencywith a given marker of about 20% or less (the given marker is within 20cM of the given marker). Put another way, closely linked locico-segregate at least 80% of the time. More preferably, therecombination frequency is 10% or less, e.g., 9%, 8%, 7%, 6%, 5%, 4%,3%, 2%, 1%, 0.5%, 0.25%, or 0.1% or less. In one typical class ofembodiments, closely linked loci are within 5 cM or less of each other.

As one of skill in the art will recognize, recombination frequencies(and, as a result, map positions) can vary depending on the map used(and the markers that are on the map). Additional markers that areclosely linked to (e.g., within about 20 cM, or more preferably withinabout 10 cM, or still more preferably within 5 cM of) the markersidentified in FIGS. 1 and 2 may readily be used for identification ofQTL for breast cancer predisposition.

Marker loci are especially useful in the present invention when they areclosely linked to target loci (e.g., QTL for breast cancer phenotypes,or, alternatively, simply other marker loci that are, themselves linkedto such QTL) that they are being used as markers for. The more closely amarker is linked to a target locus that encodes or affects a phenotypictrait, the better an indicator for the target locus that the marker is(due to the reduced cross-over frequency between the target locus andthe marker). Thus, in one embodiment, closely linked loci such as amarker locus and a second locus (e.g., a given marker locus of FIGS. 1and 2 and an additional second locus) display an inter-locus cross-overfrequency of about 20% or less, e.g., 15% or less, preferably 10% orless, more preferably about 9% or less, still more preferably about 8%or less, yet more preferably about 7% or less, still more preferablyabout 6% or less, yet more preferably about 5% or less, still morepreferably about 4% or less, yet more preferably about 3% or less, andstill more preferably about 2% or less. In highly preferred embodiments,the relevant loci (e.g., a marker locus and a target locus such as aQTL) display a recombination a frequency of about 1% or less, e.g.,about 0.75% or less, more preferably about 0.5% or less, or yet morepreferably about 0.25% or 0.1% or less. Thus, the loci are about 20 cM,19 cM, 18 cM, 17 cM, 16 cM, 15 cM, 14 cM, 13 cM, 12 cM, 11 cM, 10 cM, 9cM, 8 cM, 7 cM, 6 cM, 5 cM, 4 cM, 3 cM, 2 cM, 1 cM, 0.75 cM, 0.5 cM,0.25 cM, 0 or 0.1 cM or less apart. Put another way, two loci that arelocalized to the same chromosome, and at such a distance thatrecombination between the two loci occurs at a frequency of less than20% (e.g., about 19%, 18%, 17%, 16%, 15%, 14%, 13%, 12%, 11%, 10%, 9%,8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, 0.75%, 0.5%, 0.25%, 0.1% or less) aresaid to be “proximal to” each other. In one aspect, linked markers arewithin 100 kb (which correlates in humans to about 0.1 cM, depending onlocal recombination rate), e.g., 50 kb, or even 20 kb or less of eachother.

When referring to the relationship between two genetic elements, such asa genetic element contributing to breast cancer, and a proximal marker,“coupling” phase linkage indicates the state where the “favorable”allele at the locus is physically associated on the same chromosomestrand as the “favorable” allele of the respective linked marker locus.In coupling phase, both favorable alleles are inherited together byprogeny that inherit that chromosome strand. In “repulsion” phaselinkage, the “favorable” allele at the locus of interest (e.g., a QTLfor breast cancer) is physically linked with an “unfavorable” allele atthe proximal marker locus, and the two “favorable” alleles are notinherited together (i.e., the two loci are “out of phase” with eachother).

In addition to tracking SNP and other polymorphisms in the genome, andin corresponding expressed nucleic acids and polypeptides, expressionlevel differences between individuals or populations for the geneproducts of FIGS. 1 and 2, in either mRNA or protein form, can alsocorrelate to breast cancer. Accordingly, markers of the invention caninclude any of, e.g.: genomic loci, transcribed nucleic acids, splicednucleic acids, expressed proteins, levels of transcribed nucleic acids,levels of spliced nucleic acids, and levels of expressed proteins.

Marker Amplification Strategies

Amplification primers for amplifying markers (e.g., marker loci) andsuitable probes to detect such markers or to genotype a sample withrespect to multiple marker alleles, are a feature of the invention. InFIGS. 1 and 2, specific loci for amplification are provided, along withknown flanking sequences in the design of such primers. For example,primer selection for long-range PCR is described in U.S. Ser. No.10/042,406, filed Jan. 9, 2002 and U.S. Ser. No. 10/236,480, filed Sep.5, 2002; for short-range PCR, U.S. Ser. No. 10/341,832, filed Jan. 14,2003 provides guidance with respect to primer selection. Also, there arepublicly available programs such as “Oligo” available for primer design.With such available primer selection and design software, the publiclyavailable human genome sequence and the polymorphism locations asprovided in FIGS. 1 and 2, one of skill can construct primers to amplifythe SNPs of the present invention. Further, it will be appreciated thatthe precise probe to be used for detection of a nucleic acid comprisinga SNP (e.g., an amplicon comprising the SNP) can vary, e.g., any probethat can identify the region of a marker amplicon to be detected can beused in conjunction with the present invention. Further, theconfiguration of the detection probes can, of course, vary. Thus, theinvention is not limited to the sequences recited herein.

Indeed, it will be appreciated that amplification is not a requirementfor marker detection—for example, one can directly detect unamplifiedgenomic DNA simply by performing a Southern blot on a sample of genomicDNA. Procedures for performing Southern blotting, standard amplification(PCR, LCR, or the like) and many other nucleic acid detection methodsare well established and are taught, e.g., in Sambrook et al., MolecularCloning—A Laboratory Manual (3rd Ed.), Vol. 1-3, Cold Spring HarborLaboratory, Cold Spring Harbor, N.Y., 2000 (“Sambrook”); CurrentProtocols in Molecular Biology, F. M. Ausubel et al., eds., CurrentProtocols, a joint venture between Greene Publishing Associates, Inc.and John Wiley & Sons, Inc., (supplemented through 2002) (“Ausubel”))and PCR Protocols A Guide to Methods and Applications (Innis et al. eds)Academic Press Inc. San Diego, Calif. (1990) (Innis).

Separate detection probes can also be omitted in amplification/detectionmethods, e.g., by performing a real time amplification reaction thatdetects product formation by modification of the relevant amplificationprimer upon incorporation into a product, incorporation of labelednucleotides into an amplicon, or by monitoring changes in molecularrotation properties of amplicons as compared to unamplified precursors(e.g., by fluorescence polarization).

Typically, molecular markers are detected by any established methodavailable in the art, including, without limitation, allele specifichybridization (ASH), detection of single nucleotide extension, arrayhybridization (optionally including ASH), or other methods for detectingsingle nucleotide polymorphisms (SNPs), amplified fragment lengthpolymorphism (AFLP) detection, amplified variable sequence detection,randomly amplified polymorphic DNA (RAPD) detection, restrictionfragment length polymorphism (RFLP) detection, self-sustained sequencereplication detection, simple sequence repeat (SSR) detection,single-strand conformation polymorphisms (SSCP) detection, isozymemarker detection, northern analysis (where expression levels are used asmarkers), quantitative amplification of mRNA or cDNA, or the like. Whilethe exemplary markers provided in the Figures are SNP markers, any ofthe aforementioned marker types can be employed in the context of theinvention to identify linked loci that correlate with a breast cancerphenotype.

Example Techniques for Marker Detection

The invention provides molecular markers that comprise or are linked toQTL for breast cancer phenotypes. The markers find use in diseasepredisposition diagnosis, prognosis, treatment, etc. It is not intendedthat the invention be limited to any particular method for the detectionof these markers.

Markers corresponding to genetic polymorphisms between members of apopulation can be detected by numerous methods well-established in theart (e.g., PCR-based sequence specific amplification, restrictionfragment length polymorphisms (RFLPs), isozyme markers, northernanalysis, allele specific hybridization (ASH), array basedhybridization, amplified variable sequences of the genome,self-sustained sequence replication, simple sequence repeat (SSR),single nucleotide polymorphism (SNP), random amplified polymorphic DNA(“RAPD”) or amplified fragment length polymorphisms (AFLP). In oneadditional embodiment, the presence or absence of a molecular marker isdetermined simply through nucleotide sequencing of the polymorphicmarker region. Any of these methods are readily adapted to highthroughput analysis.

Some techniques for detecting genetic markers utilize hybridization of aprobe nucleic acid to nucleic acids corresponding to the genetic marker(e.g., amplified nucleic acids produced using genomic DNA as atemplate). Hybridization formats, including, but not limited to:solution phase, solid phase, mixed phase, or in situ hybridizationassays are useful for allele detection. An extensive guide to thehybridization of nucleic acids is found in Tijssen (1993) LaboratoryTechniques in Biochemistry and Molecular Biology—Hybridization withNucleic Acid Probes Elsevier, N.Y., as well as in Sambrook, Berger andAusubel.

For example, markers that comprise restriction fragment lengthpolymorphisms (RFLP) are detected, e.g., by hybridizing a probe which istypically a subfragment (or a synthetic oligonucleotide corresponding toa sub-fragment) of the nucleic acid to be detected to restrictiondigested genomic DNA. The restriction enzyme is selected to providerestriction fragments of at least two alternative (or polymorphic)lengths in different individuals or populations. Determining one or morerestriction enzyme that produces informative fragments for each alleleof a marker is a simple procedure, well known in the art. Afterseparation by length in an appropriate matrix (e.g., agarose orpolyacrylamide) and transfer to a membrane (e.g., nitrocellulose, nylon,etc.), the labeled probe is hybridized under conditions which result inequilibrium binding of the probe to the target followed by removal ofexcess probe by washing.

Nucleic acid probes to the marker loci can be cloned and/or synthesized.Any suitable label can be used with a probe of the invention. Detectablelabels suitable for use with nucleic acid probes include, for example,any composition detectable by spectroscopic, radioisotopic,photochemical, biochemical, immunochemical, electrical, optical orchemical means. Useful labels include biotin for staining with labeledstreptavidin conjugate, magnetic beads, fluorescent dyes, radiolabels,enzymes, and colorimetric labels. Other labels include ligands whichbind to antibodies labeled with fluorophores, chemiluminescent agents,and enzymes. A probe can also constitute radiolabelled PCR primers thatare used to generate a radiolabelled amplicon. Labeling strategies forlabeling nucleic acids and corresponding detection strategies can befound, e.g., in Haugland (2003) Handbook of Fluorescent Probes andResearch Chemicals Ninth Edition by Molecular Probes, Inc. (EugeneOreg.). Additional details regarding marker detection strategies arefound below.

Amplification-Based Detection Methods

PCR, RT-PCR and LCR are in particularly broad use as amplification andamplification-detection methods for amplifying nucleic acids of interest(e.g., those comprising marker loci), facilitating detection of thenucleic acids of interest. Details regarding the use of these and otheramplification methods can be found in any of a variety of standardtexts, including, e.g., Sambrook, Ausubel, and Berger. Many availablebiology texts also have extended discussions regarding PCR and relatedamplification methods. One of skill will appreciate that essentially anyRNA can be converted into a double stranded DNA suitable for restrictiondigestion, PCR expansion and sequencing using reverse transcriptase anda polymerase (“Reverse Transcription-PCR, or “RT-PCR”). See also,Ausubel, Sambrook and Berger, above. These methods can also be used toquantitatively amplify mRNA or corresponding cDNA, providing anindication of expression levels of mRNA that correspond to a geneproduct corresponding to the genes or gene products of FIGS. 1 and 2 inan individual. Differences in expression levels for these genes betweenindividuals, families, lines and/or populations can be used as markersfor breast cancer phenotypes.

Real Time Amplification/Detection Methods

In one aspect, real time PCR or LCR is performed on the amplificationmixtures described herein, e.g., using molecular beacons or TaqMan™probes. A molecular beacon (MB) is an oligonucleotide or PNA which,under appropriate hybridization conditions, self-hybridizes to form astem and loop structure. The MB has a label and a quencher at thetermini of the oligonucleotide or PNA; thus, under conditions thatpermit intra-molecular hybridization, the label is typically quenched(or at least altered in its fluorescence) by the quencher. Underconditions where the MB does not display intra-molecular hybridization(e.g., when bound to a target nucleic acid, e.g., to a region of anamplicon during amplification), the MB label is unquenched. Detailsregarding standard methods of making and using MBs are well establishedin the literature and MBs are available from a number of commercialreagent sources. See also, e.g., Leone et al. (1995) “Molecular beaconprobes combined with amplification by NASBA enable homogenous real-timedetection of RNA.” Nucleic Acids Res. 26:2150-2155; Tyagi and Kramer(1996) “Molecular beacons: probes that fluoresce upon hybridization”Nature Biotechnology 14:303-308; Blok and Kramer (1997) “Amplifiablehybridization probes containing a molecular switch” Mol Cell Probes11:187-194; Hsuih et al. (1997) “Novel, ligation dependent PCR assay fordetection of hepatitis C in serum” J Clin Microbiol 34:501-507;Kostrikis et al. (1998) “Molecular beacons: spectral genotyping of humanalleles” Science 279:1228-1229; Sokol et al. (1998) “Real time detectionof DNA:RNA hybridization in living cells” Proc. Natl. Acad. Sci. U.S.A.95:11538-11543; Tyagi et al. (1998) “Multicolor molecular beacons forallele discrimination” Nature Biotechnology 16:49-53; Bonnet et al.(1999) “Thermodynamic basis of the chemical specificity of structuredDNA probes” Proc. Natl. Acad. Sci. U.S.A. 96:6171-6176; Fang et al.(1999) “Designing a novel molecular beacon for surface-immobilized DNAhybridization studies” J. Am. Chem. Soc. 121:2921-2922; Marras et al.(1999) “Multiplex detection of single-nucleotide variation usingmolecular beacons” Genet. Anal. Biomol. Eng. 14:151-156; and Vet et al.(1999) “Multiplex detection of four pathogenic retroviruses usingmolecular beacons” Proc. Natl. Acad. Sci. U.S.A. 96:6394-6399.Additional details regarding MB construction and use is found in thepatent literature, e.g., U.S. Pat. No. 5,925,517 (Jul. 20, 1999) toTyagi et al. entitled “Detectably labeled dual conformationoligonucleotide probes, assays and kits;” U.S. Pat. No. 6,150,097 toTyagi et al (Nov. 21, 2000) entitled “Nucleic acid detection probeshaving non-FRET fluorescence quenching and kits and assays includingsuch probes” and U.S. Pat. No. 6,037,130 to Tyagi et al (Mar. 14, 2000),entitled “Wavelength-shifting probes and primers and their use in assaysand kits.”

PCR detection and quantification using dual-labeled fluorogenicoligonucleotide probes, commonly referred to as “TaqMan™” probes, canalso be performed according to the present invention. These probes arecomposed of short (e.g., 20-25 base) oligodeoxynucleotides that arelabeled with two different fluorescent dyes. On the 5′ terminus of eachprobe is a reporter dye, and on the 3′ terminus of each probe aquenching dye is found. The oligonucleotide probe sequence iscomplementary to an internal target sequence present in a PCR amplicon.When the probe is intact, energy transfer occurs between the twofluorophores and emission from the reporter is quenched by the quencherby FRET. During the extension phase of PCR, the probe is cleaved by 5′nuclease activity of the polymerase used in the reaction, therebyreleasing the reporter from the oligonucleotide-quencher and producingan increase in reporter emission intensity. Accordingly, TaqMan™ probesare oligonucleotides that have a label and a quencher, where the labelis released during amplification by the exonuclease action of thepolymerase used in amplification. This provides a real time measure ofamplification during synthesis. A variety of TaqMan™ reagents arecommercially available, e.g., from Applied Biosystems (DivisionHeadquarters in Foster City, Calif.) as well as from a variety ofspecialty vendors such as Biosearch Technologies (e.g., black holequencher probes). Further details regarding dual-label probe strategiescan be found, e.g., in WO92/02638.

Other similar methods include e.g. fluorescence resonance energytransfer between two adjacently hybridized probes, e.g., using the“LightCycler®” format described in U.S. Pat. No. 6,174,670.

Array-Based Marker Detection

Array-based detection can be performed using commercially availablearrays, e.g., from Affymetrix (Santa Clara, Calif.) or othermanufacturers. Reviews regarding the operation of nucleic acid arraysinclude Sapolsky et al. (1999) “High-throughput polymorphism screeningand genotyping with high-density oligonucleotide arrays.” GeneticAnalysis: Biomolecular Engineering 14:187-192; Lockhart (1998) “Mutantyeast on drugs” Nature Medicine 4:1235-1236; Fodor (1997) “Genes, Chipsand the Human Genome.” FASEB Journal 11:A879; Fodor (1997) “MassivelyParallel Genomics.” Science 277: 393-395; and Chee et al. (1996)“Accessing Genetic Information with High-Density DNA Arrays.” Science274:610-614. Array based detection is a preferred method foridentification markers of the invention in samples, due to theinherently high-throughput nature of array based detection.

A variety of probe arrays have been described in the literature and canbe used in the context of the present invention for detection of markersthat can be correlated to the phenotypes noted herein. For example, DNAprobe array chips or larger DNA probe array wafers (from whichindividual chips would otherwise be obtained by breaking up the wafer)are used in one embodiment of the invention. DNA probe array wafersgenerally comprise glass wafers on which high density arrays of DNAprobes (short segments of DNA) have been placed. Each of these waferscan hold, for example, approximately 60 million DNA probes that are usedto recognize longer sample DNA sequences (e.g., from individuals orpopulations, e.g., that comprise markers of interest). The recognitionof sample DNA by the set of DNA probes on the glass wafer takes placethrough DNA hybridization. When a DNA sample hybridizes with an array ofDNA probes, the sample binds to those probes that are complementary tothe sample DNA sequence. By evaluating to which probes the sample DNAfor an individual hybridizes more strongly, it is possible to determinewhether a known sequence of nucleic acid is present or not in thesample, thereby determining whether a marker found in the nucleic acidis present. One can also use this approach to perform ASH, bycontrolling the hybridization conditions to permit single nucleotidediscrimination, e.g., for SNP identification and for genotyping a samplefor one or more SNPs. Arrays provide one convenient embodiment fordetecting multiple polymorphic markers simultaneously (or in series).For example, breast cancer susceptibility detection arrays can beconstructed in which any or all of the polymorphisms noted herein (orpolymorphisms linked thereto) are detected simultaneously to assign abreast cancer susceptibility phenotype. Of course, any detectiontechnology (PCR, LCR, real-time PCR, etc.) can similarly be used, e.g.,with multiplex amplification/detection reactions, or simply by runningseveral separate reactions, e.g., simultaneously or in series.

The use of DNA probe arrays to obtain allele information typicallyinvolves the following general steps: design and manufacture of DNAprobe arrays, preparation of the sample, hybridization of sample DNA tothe array, detection of hybridization events and data analysis todetermine sequence. Preferred wafers are manufactured using a processadapted from semiconductor manufacturing to achieve cost effectivenessand high quality, and are available, e.g., from Affymetrix, Inc of SantaClara, Calif.

For example, probe arrays can be manufactured by light-directed chemicalsynthesis processes, which combine solid-phase chemical synthesis withphotolithographic fabrication techniques as employed in thesemiconductor industry. Using a series of photolithographic masks todefine chip exposure sites, followed by specific chemical synthesissteps, the process constructs high-density arrays of oligonucleotides,with each probe in a predefined position in the array. Multiple probearrays can be synthesized simultaneously on a large glass wafer. Thisparallel process enhances reproducibility and helps achieve economies ofscale.

Once fabricated, DNA probe arrays can be used to obtain data regardingpresence and/or expression levels for markers of interest. The DNAsamples may be tagged with biotin and/or a fluorescent reporter group bystandard biochemical methods. The labeled samples are incubated with anarray, and segments of the samples bind, or hybridize, withcomplementary sequences on the array. The array can be washed and/orstained to produce a hybridization pattern. The array is then scannedand the patterns of hybridization are detected by emission of light fromthe fluorescent reporter groups. Additional details regarding theseprocedures are found in the examples below. Because the identity andposition of each probe on the array is known, the nature of the DNAsequences in the sample applied to the array can be determined. Whenthese arrays are used for genotyping experiments, they can be referredto as genotyping arrays. As already noted, the genotype of any or all ofthe polymorphisms noted herein, e.g., in FIG. 1 and/or FIG. 2 can bedetected, e.g., to assign a breast cancer predisposition phenotype.

The nucleic acid sample to be analyzed is isolated, amplified and,typically, labeled with biotin and/or a fluorescent reporter group. Thelabeled nucleic acid sample is then incubated with the array using afluidics station and hybridization oven. The array can be washed and orstained or counter-stained, as appropriate to the detection method.After hybridization, washing and staining, the array is inserted into ascanner, where patterns of hybridization are detected. The hybridizationdata are collected as light emitted from the fluorescent reporter groupsalready incorporated into the labeled nucleic acid, which is now boundto the probe array. Probes that most clearly match the labeled nucleicacid produce stronger signals than those that have mismatches. Since thesequence and position of each probe on the array are known, bycomplementarity, the identity of the nucleic acid sample applied to theprobe array can be identified.

In one embodiment, two DNA samples may be differentially labeled andhybridized with a single set of the designed genotyping arrays. In thisway two sets of data can be obtained from the same physical arrays.Labels that can be used include, but are not limited to, cychrome,fluorescein, or biotin (later stained with phycoerythrin-streptavidinafter hybridization). Two-color labeling is described in U.S. Pat. No.6,342,355, incorporated herein by reference in its entirety. Each arraymay be scanned such that the signal from both labels is detectedsimultaneously, or may be scanned twice to detect each signalseparately.

Intensity data is collected by the scanner for all the markers for eachof the individuals that are tested for presence of the marker. Themeasured intensities are a measure indicative of the amount of aparticular marker present in the sample for a given individual(expression level and/or number of copies of the allele present in anindividual, depending on whether genomic or expressed nucleic acids areanalyzed). This can be used to determine whether the individual ishomozygous or heterozygous for the marker of interest. The intensitydata is processed to provide corresponding marker information for thevarious intensities.

Additional Details Regarding Amplified Variable Sequences, SSR, AFLP,ASH, SNPs and Isozyme Markers

Amplified variable sequences refer to amplified sequences of the genomewhich exhibit high nucleic acid residue variability between members ofthe same species. All organisms have variable genomic sequences and eachorganism (with the exception of a clone, e.g., a cloned cell) has adifferent set of variable sequences. Once identified, the presence ofspecific variable sequence can be used to predict phenotypic traits.Preferably, DNA from the genome serves as a template for amplificationwith primers that flank a variable sequence of DNA. The variablesequence is amplified and then sequenced.

Alternatively, self-sustained sequence replication can be used toidentify genetic markers. Self-sustained sequence replication refers toa method of nucleic acid amplification using target nucleic acidsequences which are replicated exponentially, in vitro, undersubstantially isothermal conditions by using three enzymatic activitiesinvolved in retroviral replication: (1) reverse transcriptase, (2) RnaseH, and (3) a DNA-dependent RNA polymerase (Guatelli et al. (1990) ProcNatl Acad Sci USA 87:1874). By mimicking the retroviral strategy of RNAreplication by means of cDNA intermediates, this reaction 25 accumulatescDNA and RNA copies of the original target.

Amplified fragment length polymorphisms (AFLP) can also be used asgenetic markers (Vos et al. (1995) Nucl Acids Res 23:4407). The phrase“amplified fragment length polymorphism” refers to selected restrictionfragments which are amplified before or after cleavage by a restrictionendonuclease. The amplification step allows easier detection of specificrestriction fragments. AFLP allows the detection large numbers ofpolymorphic markers and has been used for genetic mapping (Becker et al.(1995) Mol Gen Genet 249:65; and Meksem et al. (1995) Mol Gen Genet249:74).

Allele-specific hybridization (ASH) can be used to identify the geneticmarkers of the invention. ASH technology is based on the stableannealing of a short, single-stranded, oligonucleotide probe to acompletely complementary single-strand target nucleic acid. Detectionmay be accomplished via an isotopic or non-isotopic label attached tothe probe.

For each polymorphism, two or more different ASH probes are designed tohave identical DNA sequences except at the polymorphic nucleotides. Eachprobe will have exact homology with one allele sequence so that therange of probes can distinguish all the known alternative allelesequences. Each probe is hybridized to the target DNA. With appropriateprobe design and hybridization conditions, a single-base mismatchbetween the probe and target DNA will prevent hybridization. In thismanner, only one of the alternative probes will hybridize to a targetsample that is homozygous or homogenous for an allele. Samples that areheterozygous or heterogeneous for two alleles will hybridize to both oftwo alternative probes.

ASH markers are used as dominant markers where the presence or absenceof only one allele is determined from hybridization or lack ofhybridization by only one probe. The alternative allele may be inferredfrom the lack of hybridization. ASH probe and target molecules areoptionally RNA or DNA; the target molecules are any length ofnucleotides beyond the sequence that is complementary to the probe; theprobe is designed to hybridize with either strand of a DNA target; theprobe ranges in size to conform to variously stringent hybridizationconditions, etc.

PCR allows the target sequence for ASH to be amplified from lowconcentrations of nucleic acid in relatively small volumes. Otherwise,the target sequence from genomic DNA is digested with a restrictionendonuclease and size separated by gel electrophoresis. Hybridizationstypically occur with the target sequence bound to the surface of amembrane or, as described in U.S. Pat. No. 5,468,613, the ASH probesequence may be bound to a membrane.

In one embodiment, ASH data are typically obtained by amplifying nucleicacid fragments (amplicons) from genomic DNA using PCR, transferring theamplicon target DNA to a membrane in a dot-blot format, hybridizing alabeled oligonucleotide probe to the amplicon target, and observing thehybridization dots by autoradiography.

Single nucleotide polymorphisms (SNP) are markers that consist of ashared sequence differentiated on the basis of a single nucleotide.Typically, this distinction is detected by differential migrationpatterns of an amplicon comprising the SNP on e.g., an acrylamide gel.However, alternative modes of detection, such as hybridization, e.g.,ASH, or RFLP analysis or array based detection are also appropriate.

Isozyme markers can be employed as genetic markers, e.g., to trackisozyme markers linked to the markers herein. Isozymes are multipleforms of enzymes that differ from one another in their amino acid, andtherefore their nucleic acid sequences. Some isozymes are multimericenzymes contain slightly different subunits. Other isozymes are eithermultimeric or monomeric but have been cleaved from the proenzyme atdifferent sites in the amino acid sequence. Isozymes can becharacterized and analyzed at the protein level, or alternatively,isozymes which differ at the nucleic acid level can be determined. Insuch cases any of the nucleic acid based methods described herein can beused to analyze isozyme markers.

Additional Details Regarding Nucleic Acid Amplification

As noted, nucleic acid amplification techniques such as PCR and LCR arewell known in the art and can be applied to the present invention toamplify and/or detect nucleic acids of interest, such as nucleic acidscomprising marker loci. Examples of techniques sufficient to directpersons of skill through such in vitro methods, including the polymerasechain reaction (PCR), the ligase chain reaction (LCR), Qβ-replicaseamplification and other RNA polymerase mediated techniques (e.g.,NASBA), are found in the references noted above, e.g., Innis, Sambrook;Ausubel, and Berger. Additional details are found in Mullis et al.(1987) U.S. Pat. No.4,683,202; Amheim & Levinson (Oct. 1, 1990) C&EN36-47; The Journal Of NIH Research (1991) 3, 81-94; (Kwoh et al. (1989)Proc. Natl. Acad. Sci. USA 86, 1173; Guatelli et al. (1990) Proc. Natl.Acad. Sci. USA 87, 1874; Lomell et al. (1989) J. Clin. Chem 35, 1826;Landegren et al., (1988) Science 241, 5 1077-1080; Van Brunt (1990)Biotechnology 8, 291-294; Wu and Wallace, (1989) Gene 4, 560; Barringeret al. (1990) Gene 89, 117, and Sooknanan and Malek (1995) Biotechnology13: 563-564. Improved methods of amplifying large nucleic acids by PCR,which is useful in the context of positional cloning of genes linked tothe polymorphisms herein (FIGS. 1 and/or 2), are further summarized inCheng et al. (1994) Nature 369: 684, and the references therein, inwhich PCR amplicons of up to 40 kb are generated. Methods for long-rangePCR are disclosed, for example, in U.S. patent application Ser. No.10/042,406, filed Jan. 9, 2002, entitled “Algorithms for Selection ofPrimer Pairs”; U.S. patent application Ser. No. 10/236,480, filed Sep.9, 2002, entitled “Methods for Amplification of Nucleic Acids”; and U.S.Pat. No. 6,740,510, issued May 25, 2004, entitled “Methods for 15Amplification of Nucleic Acids”. U.S. Ser. No. 10/341,832 (filed Nov.14, 2003) also provides details regarding primer picking methods forperforming short range PCR.

Detection of Protein Expression Products

Proteins such as those encoded by the genes noted in FIGS. 1 and/or 2are encoded by nucleic acids, including those comprising markers thatare correlated to the phenotypes of interest herein. For a descriptionof the basic paradigm of molecular biology, including the expression(transcription and/or translation) of DNA into RNA into protein, see,Alberts et al. (2002) Molecular Biology of the Cell, 4th Edition Taylorand Francis, Inc., ISBN: 0815332181 (“Alberts”), and Lodish et al.(1999) Molecular Cell Biology, 4^(th) Edition W H Freeman & Co, ISBN:071673706X (“Lodish”). Accordingly, proteins corresponding to the genesin FIGS. 1 and/or 2 can be detected as markers, e.g., by detectingdifferent protein isotypes between individuals or populations, or bydetecting a differential presence, absence or expression level of such aprotein of interest (e.g., a gene product of FIGS. 1 and/or 2).

A variety of protein detection methods are known and can be used todistinguish markers. In addition to the various references noted supra,a variety of protein manipulation and detection methods are well knownin the art, including, e.g., those set forth in R. Scopes, ProteinPurification, Springer-Verlag, N.Y. (1982); Deutscher, Methods inEnzymology Vol. 182: Guide to Protein Purification, Academic Press, Inc.N.Y. (1990); Sandana (1997) Bioseparation of Proteins, Academic Press,Inc.; Bollag et al. (1996) Protein Methods, 2nd Edition Wiley-Liss, NY;Walker (1996) The Protein Protocols Handbook Humana Press, NJ, Harrisand Angal (1990) Protein Purification Applications: A Practical ApproachIRL Press at Oxford, Oxford, England; Harris and Angal ProteinPurification Methods: A Practical Approach IRL Press at Oxford, Oxford,England; Scopes (1993) Protein Purification: Principles and Practice 3rdEdition Springer Verlag, NY; Janson and Ryden (1998) ProteinPurification: Principles, High Resolution Methods and Applications,Second Edition Wiley-VCH, NY; and Walker (1998) Protein Protocols onCD-ROM Humana Press, NJ; and the references cited therein. Additionaldetails regarding protein purification and detection methods can befound in Satinder Ahuja ed., Handbook of Bioseparations, Academic Press(2000).

“Proteomic” detection methods, which detect many proteins simultaneouslyhave been described. These can include various multidimensionalelectrophoresis methods (e.g., 2-d gel electrophoresis), massspectrometry based methods (e.g., SELDI, MALDI, electrospray, etc.), orsurface plasmon reasonance methods. For example, in MALDI, a sample isusually mixed with an appropriate matrix, placed on the surface of aprobe and examined by laser desorption/ionization. The technique ofMALDI is well known in the art. See, e.g., U.S. Pat. No. 5,045,694(Beavis et al.), U.S. Pat. No. 5,202,561 (Gleissmann et al.), and U.S.Pat. No. 6,111,251 (Hillenkamp). Similarly, for SELDI, a first aliquotis contacted with a solid support-bound (e.g., substrate-bound)adsorbent. A substrate is typically a probe (e.g., a biochip) that canbe positioned in an interrogatable relationship with a gas phase ionspectrometer. SELDI is also a well known technique, and has been appliedto diagnostic proteomics. See, e.g. Issaq et al. (2003) “SELDI-TOF MSfor Diagnostic Proteomics” Analytical Chemistry 75:149A-155A.

In general, the above methods can be used to detect different forms(alleles) of proteins and/or can be used to detect different expressionlevels of the proteins (which can be due to allelic differences) betweenindividuals, families, lines, populations, etc. Differences inexpression levels, when controlled for environmental factors, can beindicative of different alleles at a QTL for the gene of interest, evenif the encoded differentially expressed proteins are themselvesidentical. This occurs, for example, where there are multiple allelicforms of a gene in non-coding regions, e.g., regions such as promotersor enhancers that control gene expression. Thus, detection ofdifferential expression levels can be used as a method of detectingallelic differences.

In other aspect of the present invention, a gene comprising, in linkagedisequilibrium with, or under the control of a nucleic acid associatedwith a breast cancer phenotype may exhibit differential allelicexpression. “Differential allelic expression” as used herein refers toboth qualitative and quantitative differences in the allelic expressionof multiple alleles of a single gene present in a cell. As such, a genedisplaying differential allelic expression may have one allele expressedat a different time or level as compared to a second allele in the samecell/tissue. For example, an allele associated with a breast cancerphenotype may be expressed at a higher or lower level than an allelethat is not associated with the breast cancer phenotype, even thoughboth are alleles of the same gene and are present in the samecell/tissue. Differential allelic expression and analysis methods aredisclosed in detail in U.S. patent application Ser. No. 10/438,184,filed May 13, 2003 and U.S. patent application Ser. No. 10/845,316,filed May 12, 2004, both of which are entitled “Allele-specificexpression patterns.” Detection of a differential allelic expressionpattern of one or more nucleic acids, or fragments, derivatives,polymorphisms, variants or complements thereof, associated with a breastcancer phenotype is a prognostic and diagnostic forsusceptibility/resistance to breast cancer; likewise, detection of adifferential allelic expression pattern of one or more nucleic acids, orfragments, derivatives, polymorphisms, variants or complements thereof,associated with a breast cancer phenotype is prognostic for anddiagnostic of breast cancer and breast cancer treatment outcomes.

Additional Details Regarding Types of Markers Appropriate for Screening

The biological markers that are screened for correlation to thephenotypes herein can be any of those types of markers that can bedetected by screening, e.g., genetic markers such as allelic variants ofa genetic locus (e.g., as in SNPs), expression markers (e.g., presenceor quantity of mRNAs and/or proteins), and/or the like.

The nucleic acid of interest to be amplified, transcribed, translatedand/or detected in the methods of the invention can be essentially anynucleic acid, though nucleic acids derived from human sources areespecially relevant to the detection of markers associated with diseasediagnosis and clinical applications. The sequences for many nucleicacids and amino acids (from which nucleic acid sequences can be derivedvia reverse translation) are available, including for the genes/proteinsof FIGS. 1 and/or 2. Common sequence repositories for known nucleicacids include GenBank® EMBL, DDBJ and the NCBI. Other repositories caneasily be identified by searching the Internet. The nucleic acid to beamplified, transcribed, translated and/or detected can be an RNA (e.g.,where amplification includes RT-PCR or LCR, the Van-Gelder Eberwinereaction or RiboSPIA) or DNA (e.g., amplified DNA, cDNA or genomic DNA),or even any analogue thereof (e.g., for detection of synthetic nucleicacids or analogues thereof, e.g., where the sample of interest includesor is used to derive or synthesize artificial nucleic acids). Anyvariation in a nucleic acid sequence or expression level betweenindividuals or populations can be detected as a marker, e.g., amutation, a polymorphism, a single nucleotide polymorphism (SNP), anallele, an isotype, expression of an RNA or protein, etc. One can detectvariation in sequence, expression levels or gene copy numbers as markersthat can be correlated to a breast cancer phenotype.

For example, the methods of the invention are useful in screeningsamples derived from patients for a marker nucleic acid of interest,e.g., from bodily fluids (blood, saliva, urine etc.), biopsy, tissue,and/or waste from the patient. Thus, tissue biopsies, stool, sputum,saliva, blood, lymph, tears, sweat, urine, vaginal secretions,ejaculatory fluid or the like can easily be screened for nucleic acidsby the methods of the invention, as can essentially any tissue ofinterest that contains the appropriate nucleic acids. These samples aretypically taken, following informed consent, from a patient by standardmedical laboratory methods.

Prior to amplification and/or detection of a nucleic acid comprising amarker, the nucleic acid is optionally purified from the samples by anyavailable method, e.g., those taught in Berger and Kimmel, Guide toMolecular Cloning Techniques, Methods in Enzymology volume 152 AcademicPress, Inc., San Diego, Calif. (Berger); Sambrook et al., MolecularCloning—A Laboratory Manual (3rd Ed.), Vol. 1-3, Cold Spring HarborLaboratory, Cold Spring Harbor, N.Y., 2001 (“Sambrook”); and/or CurrentProtocols in Molecular Biology, F. M. Ausubel et al., eds., CurrentProtocols, a joint venture between Greene Publishing Associates, Inc.and John Wiley & Sons, Inc., (supplemented through 2002) (“Ausubel”)). Aplethora of kits are also commercially available for the purification ofnucleic acids from cells or other samples (see, e.g., EasyPrep™,FlexiPrep™, both from Pharmacia Biotech; StrataClean™, from Stratagene;and, QIAprep™ from Qiagen). Alternately, samples can simply be directlysubjected to amplification or detection, e.g., following aliquottingand/or dilution.

Examples of markers can include polymorphisms, single nucleotidepolymorphisms, presence of one or more nucleic acids in a sample,absence of one or more nucleic acids in a sample, presence of one ormore genomic DNA sequences, absence or one or more genomic DNAsequences, presence of one or more mRNAs, absence of one or more mRNAs,expression levels of one or more mRNAs, presence of one or moreproteins, expression levels of one or more proteins, and/or data derivedfrom any of the preceding or combinations thereof. Essentially anynumber of markers can be detected, using available methods, e.g., usingarray technologies that provide high density, high throughput markermapping. Thus, at least about 10, 100, 1,000, 10,000, or even 100,000 ormore genetic markers can be tested, simultaneously or in a serialfashion (or combination thereof), for correlation to a relevantphenotype, in the first and/or second population. Combinations ofmarkers can also be desirably tested, e.g., to identify geneticcombinations or combinations of expression patterns in populations thatare correlated to the phenotype.

As noted, the biological marker to be detected can be any detectablebiological component. Commonly detected markers include genetic markers(e.g., DNA sequence markers present in genomic DNA or expressionproducts thereof) and expression markers (which can reflect geneticallycoded factors, environmental factors, or both). Where the markers areexpression markers, the methods can include determining a firstexpression profile for a first individual or population (e.g., of one ormore expressed markers, e.g., a set of expressed markers) and comparingthe first expression profile to a second expression profile for thesecond individual or population. In this example, correlating expressionmarker(s) to a particular phenotype can include correlating the first orsecond expression profile to the phenotype of interest.

Probe/Primer Synthesis Methods

In general, synthetic methods for making oligonucleotides, includingprobes, primers, molecular beacons, PNAs, LNAs (locked nucleic acids),etc., are well known. For example, oligonucleotides can be synthesizedchemically according to the solid phase phosphoramidite triester methoddescribed by Beaucage and Caruthers (1981), Tetrahedron Letts., 22(20):1859-1862, e.g., using a commercially available automated synthesizer,e.g., as described in Needham-VanDevanter et al. (1984) Nucleic AcidsRes., 12:6159-6168. Oligonucleotides, including modifiedoligonucleotides can also be ordered from a variety of commercialsources known to persons of skill. There are many commercial providersof oligo synthesis services, and thus this is a broadly accessibletechnology. Any nucleic acid can be custom ordered from any of a varietyof commercial sources, such as The Midland Certified Reagent Company(mcrc@oligos.com), The Great American Gene Company (www.genco.com),ExpressGen Inc. (www.expressgen.com), Operon Technologies Inc. (Alameda,Calif.) and many others. Similarly, PNAs can be custom ordered from anyof a variety of sources, such as PeptidoGenic (pkim@ccnet.com), HTIBio-products, inc. (htibio.com), BMA Biomedicals Ltd (U.K.), Bio.Synthesis, Inc., and many others.

In Silico Marker Detection

In some embodiments, in silica methods can be used to detect the markerloci of interest. For example, the sequence of a nucleic acid comprisingthe marker locus of interest can be stored in a computer. The desiredmarker locus sequence or its homolog can be identified using anappropriate nucleic acid search algorithm as provided by, for example,in such readily available programs as BLAST, or even simple wordprocessors. The entire human genome has been sequenced and, thus,sequence information can be used to identify marker regions, flankingnucleic acids, etc.

Amplification Primers for Marker Detection

In some preferred embodiments, the molecular markers of the inventionare detected using a suitable PCR-based detection method, where the sizeor sequence of the PCR amplicon is indicative of the absence or presenceof the marker (e.g., a particular marker allele). In these types ofmethods, PCR primers are hybridized to the conserved regions flankingthe polymorphic marker region.

Suitable primers to be used with the invention can be designed using anysuitable method. It is not intended that the invention be limited to anyparticular primer or primer pair. For example, primers can be designedusing any suitable software program, such as LASER GENE®, e.g., takingaccount of publicly available sequence information. Flanking sequencesfor the polymorphisms identified herein are publicly available;accordingly, suitable amplification primers can be constructed based onwell understood base-pairing rules. The sequence of any amplicon can bedetected as has already been discussed above, e.g., by hybridization,array hybridization, PCR, real-time PCR, LCR, or the like.

In some embodiments, the primers of the invention are radiolabelled, orlabeled by any suitable means (e.g., using a non-radioactive fluorescenttag), to allow for rapid visualization of differently sized ampliconsfollowing an amplification reaction without any additional labeling stepor visualization step. In some embodiments, the primers are not labeled,and the amplicons are visualized following their size resolution, e.g.,following agarose or acrylamide gel electrophoresis. In someembodiments, ethidium bromide staining of the PCR amplicons followingsize resolution allows visualization of the different size amplicons.

It is not intended that the primers of the invention be limited togenerating an amplicon of any particular size. For example, the primersused to amplify the marker loci and alleles herein are not limited toamplifying the entire region of the relevant locus, or any subregionthereof. The primers can generate an amplicon of any suitable length fordetection. In some embodiments, marker amplification produces anamplicon at least 20 nucleotides in length, or alternatively, at least50 nucleotides in length, or alternatively, at least 100 nucleotides inlength, or alternatively, at least 200 nucleotides in length. Ampliconsof any size can be detected using the various technologies describedherein. Differences in base composition or size can be detected byconventional methods such as electrophoresis.

Detection of Markers for Positional Cloning

In some embodiments, a nucleic acid probe is used to detect a nucleicacid that comprises a marker sequence. In addition to their role indetermining breast cancer phenotypes, such probes can also be used, forexample, in positional cloning to isolate nucleotide sequences linked tothe marker nucleotide sequence. It is not intended that the nucleic acidprobes of the invention be limited to any particular size. In someembodiments, nucleic acid probe is at least 20 nucleotides in length, oralternatively, at least 50 nucleotides in length, or alternatively, atleast 100 nucleotides in length, or alternatively, at least 200nucleotides in length.

A hybridized probe is detected using, e.g., autoradiography,fluorography or other similar detection techniques depending on thelabel to be detected. Examples of specific hybridization protocols arewidely available in the art, see, e.g., Berger, Sambrook, and Ausubel,all herein.

Generation of Transgenic Cells

The present invention also provides cells which are transformed withnucleic acids corresponding to QTL identified according to theinvention. For example, such nucleic acids include chromosome intervals(e.g., genomic fragments), genes, ORFs and/or cDNAs that encode genesthat correspond or are linked to QTL for breast cancer phenotypes.Additionally, the invention provides for the production of polypeptidesthat influence breast cancer phenotypes. This is useful, e.g., toinfluence breast cancers, and for the generation of transgenic cells.These cells provide commercially useful cell lines having defined genesthat influence the relevant phenotype, thereby providing a platform forscreening potential modulators of phenotype, as well as basic researchinto the mechanism of action for each of the genes of interest. Inaddition, gene therapy can be used to introduce desirable genes intoindividuals or populations thereof. Such gene therapies may be used toprovide a treatment for a disorder exhibited by an individual, or may beused as a preventative measure to prevent the development of such adisorder in an individual at risk.

General texts which describe molecular biological techniques for thecloning and manipulation of nucleic acids and production of encodedpolypeptides include Berger and Kimmel, Guide to Molecular CloningTechniques, Methods in Enzymology volume 152 Academic Press, Inc., SanDiego, Calif. (Berger); Sambrook et al., Molecular Cloning—A LaboratoryManual (3rd Ed.), Vol. 1-3, Cold Spring Harbor Laboratory, Cold SpringHarbor, N.Y., 2001 (“Sambrook”) and Current Protocols in MolecularBiology, F. M. Ausubel et al., eds., Current Protocols, a joint venturebetween Greene Publishing Associates, Inc. and John Wiley & Sons, Inc.,(supplemented through 2004 or later) (“Ausubel”)). These texts describemutagenesis, the use of vectors, promoters and many other relevanttopics related to, e.g., the generation of clones that comprise nucleicacids of interest, e.g., genes, marker loci, marker probes, QTL thatsegregate with marker loci, etc.

Host cells are genetically engineered (e.g., transduced, transfected,transformed, etc.) with the vectors of this invention (e.g., vectors,such as expression vectors which comprise a gene or an ORF derived fromor related to a QTL) which can be, for example, a cloning vector, ashuttle vector or an expression vector. Such vectors are, for example,in the form of a plasmid, a phagemid, an agrobacterium, a virus, a nakedpolynucleotide (linear or circular), or a conjugated polynucleotide.Vectors can be introduced into bacteria, especially for the purpose ofpropagation and expansion. Additional details regarding nucleic acidintroduction methods are found in Sambrook, Berger and Ausubel, infra.The method of introducing a nucleic acid of the present invention into ahost cell is not critical to the instant invention, and it is notintended that the invention be limited to any particular method forintroducing exogenous genetic material into a host cell. Thus, anysuitable method, e.g., including but not limited to the methods providedherein, which provides for effective introduction of a nucleic acid intoa cell or protoplast can be employed and finds use with the invention.

The engineered host cells can be cultured in conventional nutrient mediamodified as appropriate for such activities as, for example, activatingpromoters or selecting transformants. In addition to Sambrook, Bergerand Ausubel, all infra, Atlas and Parks (eds) The Handbook ofMicrobiological Media (1993) CRC Press, Boca Raton, Fla. and availablecommercial literature such as the Life Science Research Cell CultureCatalogue (2004) from Sigma-Aldrich, Inc (St Louis, Mo.)(“Sigma-LSRCCC”) provide additional details.

Correlating Markers to Phenotypes

One aspect of the invention is a description of correlations betweenpolymorphisms noted in FIGS. 1 and/or 2 and breast cancer phenotypes. Anunderstanding of these correlations can be used in the present inventionto correlate information regarding a set of polymorphisms that anindividual or sample is determined to possess and a phenotype that theyare likely to display. Further, higher order correlations that accountfor combinations of alleles in one or more different genes can also beassessed for correlations to phenotype.

These correlations can be performed by any method that can identify arelationship between an allele and a phenotype, or a combination ofalleles and a combination of phenotypes. For example, alleles in genesor loci in FIGS. 1 and/or 2 can be correlated with one or more breastcancer phenotypes. Most typically, these methods involve referencing alook up table that comprises correlations between alleles of thepolymorphism and the phenotype. The table can include data for multipleallele-phenotype relationships and can take account of additive or otherhigher order effects of multiple allele-phenotype relationships, e.g.,through the use of statistical tools such as principle componentanalysis, heuristic algorithms, etc.

Correlation of a marker to a phenotype optionally includes performingone or more statistical tests for correlation. Many statistical testsare known, and most are computer-implemented for ease of analysis. Avariety of statistical methods of determining associations/correlationsbetween phenotypic traits and biological markers are known and can beapplied to the present invention. For an introduction to the topic, see,Hartl (1981) A Primer of Population Genetics Washington University,Saint Louis Sinauer Associates, Inc. Sunderland, Mass. ISBN:0-087893-271-2. A variety of appropriate statistical models aredescribed in Lynch and Walsh (1998) Genetics and Analysis ofQuantitative Traits, Sinauer Associates, Inc. Sunderland Mass. ISBN0-87893-481-2. These models can, for example, provide for correlationsbetween genotypic and phenotypic values, characterize the influence of alocus on a phenotype, sort out the relationship between environment andgenotype, determine dominance or penetrance of genes, determine maternaland other epigenetic effects, determine principle components in ananalysis (via principle component analysis, or “PCA”), and the like. Thereferences cited in these texts provides considerable further detail onstatistical models for correlating markers and phenotype.

In addition to standard statistical methods for determining correlation,other methods that determine correlations by pattern recognition andtraining, such as the use of genetic algorithms, can be used todetermine correlations between markers and phenotypes. This isparticularly useful when identifying higher order correlations betweenmultiple alleles and multiple phenotypes. To illustrate, neural networkapproaches can be coupled to genetic algorithm-type programming forheuristic development of a structure-function data space model thatdetermines correlations between genetic information and phenotypicoutcomes. For example, NNUGA (Neural Network Using Genetic Algorithms)is an available program (e.g., on the world wide web atcs.bgu.ac.il/˜omri/NNUGA which couples neural networks and geneticalgorithms. An introduction to neural networks can be found, e.g., inKevin Gurney, An Introduction to Neural Networks, UCL Press (1999) andon the world wide web at shef.ac.uk/psychology/gurney/notes/index.html.Additional useful neural network references include those noted above inregard to genetic algorithms and, e.g., Bishop, Neural Networks forPattern Recognition, Oxford University Press (1995), and Ripley et al.,Pattern Recognition and Neural Networks, Cambridge University Press(1995). Two tables showing exemplary data sets including certainstatistical analyses are shown in FIGS. 1 and/or 2.

Additional references that are useful in understanding data analysisapplications for using and establishing correlations, principlecomponents of an analysis, neural network modeling and the like,include, e.g., Hinchliffe, Modeling Molecular Structures, John Wiley andSons (1996), Gibas and Jambeck, Bioinformatics Computer Skills, O'Reilly(2001), Pevzner, Computational Molecular Biology and AlgorithmicApproach, The MIT Press (2000), Durbin et al., Biological SequenceAnalysis: Probabilistic Models of Proteins and Nucleic Acids, CambridgeUniversity Press (1998), and Rashidi and Buehler, Bioinformatic Basics:Applications in Biological Science and Medicine, CRC Press LLC (2000).

In any case, essentially any statistical test can be applied in acomputer implemented model, by standard programming methods, or usingany of a variety of “off the shelf’ software packages that perform suchstatistical analyses, including, for example, those noted above andthose that are commercially available, e.g., from Partek Incorporated(St. Peters, Mo.; www.partek.com), e.g., that provide software forpattern recognition (e.g., which provide Partek Pro 2000 PatternRecognition Software) which can be applied to genetic algorithms formultivariate data analysis, interactive visualization, variableselection, neural network & statistical modeling, etc. Relationships canbe analyzed, e.g., by Principal Components Analysis (PCA) mapped mappedscatterplots and biplots, MultiDimensional Scaling (MDS)Multi-Dimensional Scaling (MDS) mapped scatterplots, star plots, etc.Available software for performing correlation analysis includes SAS,Rand MathLab.

The marker(s), whether polymorphisms or expression patterns, can be usedfor any of a variety of genetic analyses. For example, once markers havebeen identified, as in the present case, they can be used in a number ofdifferent assays for association studies. For example, probes can bedesigned for microarrays that interrogate these markers. Other exemplaryassays include, e.g., the Taqman assays and molecular beacon assaysdescribed supra, as well as conventional PCR and/or sequencingtechniques.

Additional details regarding association studies can be found in Ser.No. 10/106,097, filed Mar. 26, 2002, entitled “Methods for GenomicAnalysis;” Ser. No. 10/042,819, filed Jan. 7, 2002, entitled “GeneticAnalysis Systems and Methods;” Ser. No. 10/286,417, filed Oct. 31, 2002,entitled “Methods for Genomic Analysis;” Ser. No. 10/768,788, filed Jan.30, 2004, entitled “Apparatus and Methods for Analyzing andCharacterizing Nucleic Acid Sequences;” Ser. No. 10/447,685, filed May28, 2003, entitled “Liver Related Disease Compositions and Methods;”Ser. No. 10/970,761, filed Oct. 20, 2004, entitled “Improved AnalysisMethods and Apparatus for Individual Genotyping” (methods for individualgenotyping); Ser. No. 10/956,224, filed Sep. 30, 2004, entitled “Methodsfor Genetic Analysis.”

In some embodiments, the marker data is used to perform associationstudies to show correlations between markers and phenotypes. This can beaccomplished by determining marker characteristics in individuals withthe phenotype of interest (i.e., individuals or populations displayingthe phenotype of interest) and comparing the allele frequency or othercharacteristics (expression levels, etc.) of the markers in theseindividuals to the allele frequency or other characteristics in acontrol group of individuals. Such marker determinations can beconducted on a genome-wide basis, or can be focused on specific regionsof the genome (e.g., haplotype blocks of interest). In one embodiment,markers that are linked to the genes or loci in FIGS. 1 and/or 2 areassessed for correlation to one or more specific breast cancerpredisposition phenotypes.

In addition to the other embodiments of the methods of the presentinvention disclosed herein, the methods additionally allow for the“dissection” of a phenotype. That is, a particular phenotypes can (andtypically do) result from two or more different genetic bases. Forexample, a susceptibility phenotype in one individual may be the resultof a “defect” (or simply a particular allele-“defect” with respect to asusceptibility phenotype is context dependent, e.g., whether thephenotype is desirable or undesirable in the individual in a givenenvironment) in a gene for in FIGS. 1 and/or 2, while the same basicphenotype in a different individual may be the result of multiple“defects” in multiple genes in FIGS. 1 and/or 2. Thus, scanning aplurality of markers (e.g., as in genome or haplotype block scanning)allows for the dissection of varying genetic bases for similar (orgraduated) phenotypes.

As described in the previous paragraph, one method of conductingassociation studies is to compare the allele frequency (or expressionlevel) of markers in individuals with a phenotype of interest (“casegroup”) to the allele frequency in a control group of individuals. Inone method, informative SNPs are used to make the SNP haplotype patterncomparison (an “informative SNP” is genetic SNP marker such as a SNP orsubset (more than one) of SNPs in a genome or haplotype block that tendsto distinguish one SNP or genome or haplotype pattern from other SNPs,genomes or haplotype patterns). The approach of using informative SNPshas an advantage over other whole genome scanning or genotyping methodsknown in the art, for instead of reading all 3 billion bases of eachindividual's genome-or even reading the 3-4 million common SNPs that maybe found-only informative SNPs from a sample population need to bedetected. Reading these particular, informative SNPs provides sufficientinformation to allow statistically accurate association data to beextracted from specific experimental populations, as described above.

Thus, in an embodiment of one method of determining geneticassociations, the allele frequency of informative SNPs is determined forgenomes of a control population that do not display the phenotype. Theallele frequency of informative SNPs is also determined for genomes of apopulation that do display the phenotype. The informative SNP allelefrequencies are compared. Allele frequency comparisons can be made, forexample, by determining the allele frequency (number of instances of aparticular allele in a population divided by the total number ofalleles) at each informative SNP location in each population andcomparing these allele frequencies. The informative SNPs displaying adifference between the allele frequency of occurrence in the controlversus case populations/groups are selected for analysis. Onceinformative SNPs are selected, the SNP haplotype block(s) that containthe informative SNPs are identified, which in turn identifies a genomicregion of interest that is correlated with the phenotype. The genomicregions can be analyzed by genetic or any biological methods known inthe art e.g., for use as drug discovery targets or as diagnosticmarkers.

Systems for Identifying Breast Cancer Phenotypes

Systems for performing the above correlations are also a feature of theinvention. Typically, the system will include system instructions thatcorrelate the presence or absence of an allele (whether detecteddirectly or, e.g., through expression levels) with a predictedphenotype. The system instructions can compare detected information asto allele sequence or expression level with a database that includescorrelations between the alleles and the relevant phenotypes. As notedabove, this database can be multidimensional, thereby includinghigher-order relationships between combinations of alleles and therelevant phenotypes. These relationships can be stored in any number oflook-up tables, e.g., taking the form of spreadsheets (e.g., Excel™spreadsheets) or databases such as an Access™, SQL™, Oracle™, Paradox™,or similar database. The system includes provisions for inputtingsample-specific information regarding allele detection information,e.g., through an automated or user interface and for comparing thatinformation to the look up tables.

Optionally, the system instructions can also include software thataccepts diagnostic information associated with any detected alleleinformation, e.g., a diagnosis that a subject with the relevant allelehas a particular phenotype. This software can be heuristic in nature,using such inputted associations to improve the accuracy of the look uptables and/or interpretation of the look up tables by the system. Avariety of such approaches, including neural networks, Markov modeling,and other statistical analysis are described above.

The invention provides data acquisition modules for detecting one ormore detectable genetic marker(s) (e.g., one or more array comprisingone or more biomolecular probes, detectors, fluid handlers, or thelike). The biomolecular probes of such a data acquisition module caninclude any that are appropriate for detecting the biological marker,e.g., oligonucleotide probes, proteins, aptamers, antibodies, etc. Thesecan include sample handlers (e.g., fluid handlers), robotics,microfluidic systems, nucleic acid or protein purification modules,arrays (e.g., nucleic acid arrays), detectors, thermocyclers orcombinations thereof, e.g., for acquiring samples, diluting oraliquoting samples, purifying marker materials (e.g., nucleic acids orproteins), amplifying marker nucleic acids, detecting amplified markernucleic acids, and the like.

For example, automated devices that can be incorporated into the systemsherein have been used to assess a variety of biological phenomena,including, e.g., expression levels of genes in response to selectedstimuli (Service (1998) “Microchips Arrays Put DNA on the Spot” Science282:396-399), high throughput DNA genotyping (Zhang et al. (1999)“Automated and Integrated System for High-Throughput DNA GenotypingDirectly from Blood” Anal. Chem. 71:1138-1145) and many others.Similarly, integrated systems for performing mixing experiments, DNAamplification, DNA sequencing and the like are also available. See,e.g., Service (1998) “Coming Soon: the Pocket DNA Sequencer” Science282: 399-401. A variety of automated system components are available,e.g., from Caliper Technologies (Hopkinton, Mass.), which utilizevarious Zymate systems, which typically include, e.g., robotics andfluid handling modules. Similarly, the common ORCA® robot, which is usedin a variety of laboratory systems, e.g., for microtiter traymanipulation, is also commercially available, e.g., from BeckmanCoulter, Inc. (Fullerton, Calif.). Similarly, commercially availablemicrofluidic systems that can be used as system components in thepresent invention include those from Agilent technologies and theCaliper Technologies. Furthermore, the patent and technical literatureincludes numerous examples of microfluidic systems, including those thatcan interface directly with microwell plates for automated fluidhandling.

Any of a variety of liquid handling and/or array configurations can beused in the systems herein. One common format for use in the systemsherein is a microtiter plate, in which the array or liquid handlerincludes a microtiter tray. Such trays are commercially available andcan be ordered in a variety of well sizes and numbers of wells per tray,as well as with any of a variety of functionalized surfaces for bindingof assay or array components. Common trays include the ubiquitous 96well plate, with 384 and 1536 well plates also in common use. Samplescan be processed in such trays, with all of the processing steps beingperformed in the trays. Samples can also be processed in microfluidicapparatus, or combinations of microtiter and microfluidic apparatus.

In addition to liquid phase arrays, components can be stored in oranalyzed on solid phase arrays. These arrays fix materials in aspatially accessible pattern (e.g., a grid of rows and columns) onto asolid substrate such as a membrane (e.g., nylon or nitrocellulose), apolymer or ceramic surface, a glass or modified silica surface, a metalsurface, or the like. Components can be accessed, e.g., byhybridization, by local rehydration (e.g., using a pipette or otherfluid handling element) and fluidic transfer, or by scraping the arrayor cutting out sites of interest on the array.

The system can also include detection apparatus that is used to detectallele information, using any of the approached noted herein. Forexample, a detector configured to detect real-time PCR products (e.g., alight detector, such as a fluorescence detector) or an array reader canbe incorporated into the system. For example, the detector can beconfigured to detect a light emission from a hybridization oramplification reaction comprising an allele of interest, wherein thelight emission is indicative of the presence or absence of the allele.Optionally, an operable linkage between the detector and a computer thatcomprises the system instructions noted above is provided, allowing forautomatic input of detected allele-specific information to the computer,which can, e.g., store the database information and/or execute thesystem instructions to compare the detected allele specific informationto the look up table.

Probes that are used to generate information detected by the detectorcan also be incorporated within the system, along with any otherhardware or software for using the probes to detect the amplicon. Thesecan include thermocycler elements (e.g., for performing PCR or LCRamplification of the allele to be detected by the probes), arrays uponwhich the probes are arrayed and/or hybridized, or the like. The fluidhandling elements noted above for processing samples, can be used formoving sample materials (e.g., template nucleic acids and/or proteins tobe detected) primers, probes, amplicons, or the like into contact withone another. For example, the system can include a set of marker probesor primers configured to detect at least one allele of one or more genesor linked loci associated with a phenotype, where the gene encodes apolymorphism in FIGS. 1 and/or 2. The detector module is configured todetect one or more signal outputs from the set of marker probes orprimers, or an amplicon produced from the set of marker probes orprimers, thereby identifying the presence or absence of the allele.

The sample to be analyzed is optionally part of the system, or can beconsidered separate from it. The sample optionally includes e.g.,genomic DNA, amplified genomic DNA, cDNA, amplified cDNA, RNA, amplifiedRNA, proteins, etc., as noted herein. In one aspect, the sample isderived from a mammal such as a human patient.

Optionally, system components for interfacing with a user are provided.For example, the systems can include a user viewable display for viewingan output of computer-implemented system instructions, user inputdevices (e.g., keyboards or pointing devices such as a mouse) forinputting user commands and activating the system, etc. Typically, thesystem of interest includes a computer, wherein the variouscomputer-implemented system instructions are embodied in computersoftware, e.g., stored on computer readable media.

Standard desktop applications such as word processing software (e.g.,Microsoft Word™ or Corel WordPerfect™) and database software (e.g.,spreadsheet software such as Microsoft Excel™, Corel Quattro Pro™, ordatabase programs such as Microsoft Access™ or Sequel™, Oracle™,Paradox™) can be adapted to the present invention by inputting acharacter string corresponding to an allele herein, or an associationbetween an allele and a phenotype. For example, the systems can includesoftware having the appropriate character string information, e.g., usedin conjunction with a user interface (e.g., a GUI in a standardoperating system such as a Windows, Macintosh or LINUX system) tomanipulate strings of characters. Specialized sequence alignmentprograms such as BLAST can also be incorporated into the systems of theinvention for alignment of nucleic acids or proteins (or correspondingcharacter strings) e.g., for identifying and relating multiple alleles.

As noted, systems can include a computer with an appropriate databaseand an allele sequence or correlation of the invention. Software foraligning sequences, as well as data sets entered into the softwaresystem comprising any of the sequences herein can be a feature of theinvention. The computer can be, e.g., a PC (Intel x86 or Pentiumchip-compatible DOS™, OS2™ WINDOWS™ WINDOWS NT™, WINDOWS95™, WINDOWS98™,WINDOWS2000, WINDOWSME, or LINUX based machine, a MACINTOSH™, Power PC,or a UNIX based (e.g., SUN™ work station or LINUX based machine) orother commercially common computer which is known to one of skill.Software for entering and aligning or otherwise manipulating sequencesis available, e.g., BLASTP and BLASTN, or can easily be constructed byone of skill using a standard programming language such as Visualbasic,Fortran, Basic, Java, or the like.

Methods of Identifying Modulators

In addition to providing various diagnostic and prognostic markers foridentifying breast cancer predisposition, etc., the invention alsoprovides methods of identifying modulators of breast cancer phenotypes.In the methods, a potential modulator is contacted to a relevant proteincorresponding to a loci in FIGS. 1 and/or 2, or to a nucleic acid thatencodes such a protein. An effect of the potential modulator on the geneor gene product is detected, thereby identifying whether the potentialmodulator modulates the underlying molecular basis for the phenotype.

In addition, the methods can include, e.g., administering one or moreputative modulator to an individual that displays a relevant phenotypeand determining whether the putative modulator modulates the phenotypein the individual, e.g., in the context of a clinical trial ortreatment. This, in turn, determines whether the putative modulator isclinically useful.

The gene or gene product that is contacted by the modulator can includeany allelic form noted herein. Allelic forms, whether genes or proteins,that positively correlate to undesirable phenotypes are preferredtargets for modulator screening.

Effects of interest that can be screened for include: (a) increased ordecreased expression of a gene or gene product in FIGS. 1 and/or 2 inthe presence of the modulator; (b) a change in the timing or location ofexpression; (c) or a change in localization of the proteinscorresponding to loci of FIGS. 1 and/or 2 in the presence of themodulator.

The precise format of the modulator screen will, of course, vary,depending on the effect(s) being detected and the equipment available.Northern analysis, quantitative RT-PCR and/or array-based detectionformats can be used to distinguish expression levels of genes notedabove. Protein expression levels can also be detected using availablemethods, such as western blotting, ELISA analysis, antibodyhybridization, BIAcore, or the like. Any of these methods can be used todistinguish changes in expression levels that result from a potentialmodulator.

Accordingly, one may screen for potential modulators for activity orexpression. For example, potential modulators (small molecules, organicmolecules, inorganic molecules, proteins, hormones, transcriptionfactors, or the like) can be contacted to a cell comprising an allele ofinterest and an effect on activity or expression (or both) of a gene orprotein corresponding to a loci in FIGS. 1 and/or 2 can be detected,e.g., via northern analysis or quantitative (optionally real time)RT-PCR, before and after application of potential expression modulators.Similarly, promoter regions of the various genes (e.g., generallysequences in the region of the start site of transcription, e.g., within5 kb of the start site, e.g., 1 kb, or less e.g., within 500 bp or 250bp or 100 bp of the start site) can be coupled to reporter constructs(CAT, beta-galactosidase, luciferase or any other available reporter)and can be similarly be tested for expression activity modulation by thepotential modulator. In either case, the assays can be performed in ahigh-throughput fashion, e.g., using automated fluid handling and/ordetection systems, in serial or parallel fashion. Similarly, activitymodulators can be tested by contacting a potential modulator to anappropriate cell using any of the activity detection methods herein,regardless of whether the activity that is detected is the result ofactivity modulation, expression modulation or both.

Biosensors for detecting modulator activity detection are also a featureof the invention. These include devices or systems that comprise a geneor gene product corresponding to a loci of FIGS. 1 and/or 2 coupled to areadout that measures or displays one or more activity of the gene orproduct. Thus, any of the above described assay components can beconfigured as a biosensor by operably coupling the appropriate assaycomponents to a readout. The readout can be optical (e.g., to detectcell markers or cell survival) electrical (e.g., coupled to a PET, aBIAcore, or any of a variety of others), spectrographic, or the like,and can optionally include a user-viewable display (e.g., a CRT oroptical viewing station). The biosensor can be coupled to robotics orother automation, e.g., microfluidic systems, that direct contact of theputative modulators to the proteins of the invention, e.g., forautomated high-throughput analysis of putative modulator activity. Alarge variety of automated systems that can be adapted to use with thebiosensors of the invention are commercially available. For example,automated systems have been made to assess a variety of biologicalphenomena, including, e.g., expression levels of genes in response toselected stimuli (Service (1998) “Microchips Arrays Put DNA on the Spot”Science 282:396-399). Laboratory systems can also perform, e.g.,repetitive fluid handling operations (e.g., pipetting) for transferringmaterial to or from reagent storage systems that comprise arrays, suchas microtiter trays or other chip trays, which are used as basiccontainer elements for a variety of automated laboratory methods.Similarly, the systems manipulate, e.g., microtiter trays and control avariety of environmental conditions such as temperature, exposure tolight or air, and the like. Many such automated systems are commerciallyavailable and are described herein, including those described above.These include various Zymate systems, ORCA® robots, microfluidicdevices, etc. For example, the LabMicrofluidic device® high throughputscreening system (HTS) by Caliper Technologies, Mountain View, Calif.can be adapted for use in the present invention to screen for modulatoractivity.

In general, methods and sensors for detecting protein expression leveland activity are available, including those taught in the variousreferences above, including R. Scopes, Protein Purification,Springer-Verlag, N.Y. (1982); Deutscher, Methods in Enzymology Vol. 182:Guide to Protein Purification, Academic Press, Inc. N.Y. (1990); Sandana(1997) Bioseparation of Proteins, Academic Press, Inc.; Bollag et al.(1996) Protein Methods, 2^(nd) Edition Wiley-Liss, NY; Walker (1996) TheProtein Protocols Handbook Humana Press, NJ, Harris and Angal (1990)Protein Purification Applications: A Practical Approach IRL Press atOxford, Oxford, England; Harris and Angal Protein Purification Methods:A Practical Approach IRL Press at Oxford, Oxford, England; Scopes (1993)Protein Purification: Principles and Practice 3rd Edition SpringerVerlag, NY; Janson and Ryden (1998) Protein Purification: Principles,High Resolution Methods and Applications, Second Edition Wiley-VCH, NY;and Walker (1998) Protein Protocols on CD-ROM Humana Press, NJ; andSatinder Ahuja ed., Handbook of Bioseparations, Academic Press (2000).“Proteomic” detection methods, which detect many proteins simultaneouslyhave been described and are also noted above, including variousmultidimensional electrophoresis methods (e.g., 2-d gelelectrophoresis), mass spectrometry based methods (e.g., SELDI, MALDI,electrospray, etc.), or surface plasmon reasonance methods. These canalso be used to track protein activity and/or expression level.

Similarly, nucleic acid expression levels (e.g., mRNA) can be detectedusing any available method, including northern analysis, quantitativeRT-PCR, or the like. References sufficient to guide one of skill throughthese methods are readily available, including Ausubel, Sambrook andBerger.

Potential modulator libraries to be screened for effects on expressionand/or activity are available. These libraries can be random, or can betargeted.

Targeted libraries include those designed using any form of a rationaldesign technique that selects scaffolds or building blocks to generatecombinatorial libraries. These techniques include a number of methodsfor the design and combinatorial synthesis of target-focused libraries,including morphing with bioisosteric transformations, analysis oftarget-specific privileged structures, and the like. In general, whereinformation regarding structure genes or gene products of FIGS. 1 and/or2, is available, likely binding partners can be designed, e.g., usingflexible docking approaches, or the like. Similarly, random librariesexist for a variety of basic chemical scaffolds. In either case, manythousands of scaffolds and building blocks for chemical libraries areavailable, including those with polypeptide, nucleic acid, carbohydrate,and other backbones. Commercially available libraries and library designservices include those offered by Chemical Diversity (San Diego,Calif.), Affymetrix (Santa Clara, Calif.), Sigma (St. Louis Mo.),ChemBridge 10 Research Laboratories (San Diego, Calif.), TimTec (Newark,Del.), Nuevolution A/S (Copenhagen, Denmark) and many others.

Kits for treatment of breast cancer phenotypes can include a modulatoridentified as noted above and instructions for administering thecompound to a patient to treat breast cancer.

Regulating Gene Expression of Genes

Gene expression (e.g., transcription and/or translation) of any genelinked to a polymorphism in FIGS. 1 and 2 can be regulated using any ofa variety of techniques known in the art. For example, gene expressioncan be inhibited using an antisense nucleic acid or an interfering RNA.Inhibition of expression in particular cell-types can be used forfurther studying the in vitro or in vivo role of these genes, and/or asa mechanism for treating a condition caused by overexpression of alinked gene, and/or for treating a dominant effect caused by aparticular allele of such a gene. Gene expression modulators are oneclass of modulators provided by the present invention, e.g., modulatorsapplied to modulate a breast cancer phenotype.

For example, use of antisense nucleic acids is well known in the art. Anantisense nucleic acid has a region of complementarity to a targetnucleic acid, e.g., a target gene, mRNA, or cDNA. Typically, a nucleicacid comprising a nucleotide sequence in a complementary, antisenseorientation with respect to a coding (sense) sequence of an endogenousgene is introduced into a cell. The antisense nucleic acid can be RNA,DNA, a PNA or any other appropriate molecule. A duplex can form betweenthe antisense sequence and its complementary sense sequence, resultingin inactivation of the gene. The antisense nucleic acid can inhibit geneexpression by forming a duplex with an RNA transcribed from the gene, byforming a triplex with duplex DNA, etc. An antisense nucleic acid can beproduced, e.g., for any gene whose coding sequence is known or can bedetermined by a number of well-established techniques (e.g., chemicalsynthesis of an antisense RNA or oligonucleotide (optionally includingmodified nucleotides and/or linkages that increase resistance todegradation or improve cellular uptake) or in vitro transcription).Antisense nucleic acids and their use are described, e.g., in U.S. Pat.No. 6,242,258 to Haselton and Alexander (Jun. 5, 2001) entitled “Methodsfor the selective regulation of DNA and RNA transcription andtranslation by photoactivation”; U.S. Pat. No. 6,500,615; U.S. Pat. No.6,498,035; U.S. Pat. No. 6,395,544; U.S. Pat. No. 5,563,050; E. Schuchet al (1991) Symp Soc. Exp Biol 45:117-127; de Lange et al., (1995) CurrTop Microbiol Immunol 197:57-75; Hamilton et al. (1995) Curr TopMicrobiol Immunol 197:77-89; Finnegan et al., (1996) Proc Natl Acad SciUSA 93:8449-8454; Uhlmann and A. Pepan (1990), Chem. Rev. 90:543; P. D.Cook (1991), Anti-Cancer Drug Design 6: 5 85; J. Goodchild, BioconjugateChem. 1 (1990) 165; and, S. L. Beaucage and R. P. Iyer (1993),Tetrahedron 49:6123; and F. Eckstein, Ed. (1991), Oligonucleotides andAnalogues—A Practical Approach, IRL Press.

Gene expression can also be inhibited by RNA silencing or interference.“RNA silencing” refers to any mechanism through which the presence of asingle-stranded or, typically, a double-stranded RNA in a cell resultsin inhibition of expression of a target gene comprising a sequenceidentical or nearly identical to that of the RNA, including, but notlimited to, RNA interference, repression of translation of a target mRNAtranscribed from the target gene without alteration of the mRNA'sstability, and transcriptional silencing (e.g., histone acetylation andheterochromatin formation leading to inhibition of transcription of thetarget mRNA).

The term “RNA interference” (“RNAi,” sometimes called RNA-mediatedinterference, post-transcriptional gene silencing, or quelling) refersto a phenomenon in which the presence of RNA, typically double-strandedRNA, in a cell results in inhibition of expression of a gene comprisinga sequence identical, or nearly identical, to that of thedouble-stranded RNA. The double-stranded RNA responsible for inducingRNAi is called an “interfering RNA.” Expression of the gene is inhibitedby the mechanism of RNAi as described below, in which the presence ofthe interfering RNA results in degradation of mRNA transcribed from thegene and thus in decreased levels of the mRNA and any encoded protein.

The mechanism of RNAi has been and is being extensively investigated ina number of eukaryotic organisms and cell types. See, for example, thefollowing reviews: McManus and Sharp (2002) “Gene silencing in mammalsby small interfering RNAs” Nature Reviews Genetics 3:737-747; Hutvagnerand Zamore (2002) “RNAi: Nature abhors a double strand” Curr Opin Genet& Dev 200:225-232; Hannon (2002) “RNA interference” Nature 418:244-251;Agami (2002) “RNAi and related mechanisms and their potential use fortherapy” Curr Opin Chem Biol 6:829-834; Tuschl and Borkhardt (2002)“Small interfering RNAs: A revolutionary tool for the analysis of genefunction and gene therapy” Molecular Interventions 2:158-167; Nishikura(2001) “A short primer on RNAi: RNAdirected RNA polymerase acts as a keycatalyst” Cell 107:415-418; and Zamore (2001) “RNA interference:Listening to the sound of silence” Nature Structural Biology 8:746-750.RNAi is also described in the patent literature; see, e.g., CA 2359180by Kreutzer and Limmer entitled “Method and medicament for inhibitingthe expression of a given gene”; WO 01/68836 by Beach et al. entitled“Methods and compositions for RNA interference”; WO 01/70949 by Grahamet al. entitled “Genetic silencing”; and WO 01/75164 by Tuschl et al.entitled “RNA sequence-specific mediators of RNA interference.”

In brief, double-stranded RNA introduced into a cell (e.g., into thecytoplasm) is processed, for example by an RNAse III-like enzyme calledDicer, into shorter double-stranded fragments called small interferingRNAs (siRNAs, also called short interfering RNAs). The length and natureof the siRNAs produced is dependent on the species of the cell, althoughtypically siRNAs are 21-25 nucleotides long (e.g., an siRNA may have a19 base pair duplex portion with two nucleotide 3′ overhangs at eachend). Similar siRNAs can be produced in vitro (e.g., by chemicalsynthesis or in vitro transcription) and introduced into the cell toinduce RNAi. The siRNA becomes associated with an RNA-induced silencingcomplex (RISC). Separation of the sense and antisense strands of thesiRNA, and interaction of the siRNA antisense strand with its targetmRNA through complementary base-pairing interactions, optionally occurs.Finally, the mRNA is cleaved and degraded.

Expression of a target gene in a cell can thus be specifically inhibitedby introducing an appropriately chosen double-stranded RNA into thecell. Guidelines for design of suitable interfering RNAs are known tothose of skill in the art. For example, interfering RNAs are typicallydesigned against exon sequences, rather than intrans or untranslatedregions. Characteristics of high efficiency interfering RNAs may vary bycell type. For example, although siRNAs may require 3′ overhangs and 5′phosphates for most efficient induction of RNAi in Drosophila cells, inmammalian cells blunt ended siRNAs and/or RNAs lacking 5′ phosphates caninduce RNAi as effectively as siRNAs with 3′ overhangs and/or 5′phosphates (see, e.g., Czauderna et al. (2003) “Structural variationsand stabilizing modifications of synthetic siRNAs in mammalian cells”Nucl Acids Res 31:2705-2716). As another example, since double-strandedRNAs greater than 30-80 base pairs long activate the antiviralinterferon response in mammalian cells and result in nonspecificsilencing, interfering RNAs for use in mammalian cells are typicallyless than 30 base pairs (for example, Caplen et al. (2001) “Specificinhibition of gene expression by small double-stranded RNAs ininvertebrate and vertebrate systems” Proc. Natl. Acad. Sci. USA98:9742-9747, Elbashir et al. (2001) “Duplexes of 21-nucleotide RNAsmediate RNA interference in cultured mammalian cells” Nature 411:494-498and Elbashir et al. (2002) “Analysis of gene function in somaticmammalian cells using small interfering RNAs” Methods 26: 199-213describe the use of 21 nucleotide siRNAs to specifically inhibit geneexpression in mammalian cell lines, and Kim et al. (2005) “SyntheticdsRNA Dicer substrates enhance RNAi potency and efficacy” NatureBiotechnology 23:222-226 describes use of 25-30 nucleotide duplexes).The sense and antisense strands of a siRNA are typically, but notnecessarily, completely complementary to each other over thedouble-stranded region of the siRNA (excluding any overhangs). Theantisense strand is typically completely complementary to the targetmRNA over the same region, although some nucleotide substitutions can betolerated (e.g., a one or two nucleotide mismatch between the antisensestrand and the mRNA can still result in RNAi, although at reducedefficiency). The ends of the double-stranded region are typically moretolerant to substitution than the middle; for example, as little as 15bp (base pairs) of complementarity between the antisense strand and thetarget mRNA in the context of a 21 mer with a 19 bp doublestrandedregion has been shown to result in a functional siRNA (see, e.g.,Czaudema et al. (2003) “Structural variations and stabilizingmodifications of synthetic siRNAs in mammalian cells” Nucl Acids Res31:2705-2716). Any overhangs can but need not be complementary to thetarget mRNA; for example, TT (two 2′-deoxythymidines) overhangs arefrequently used to reduce synthesis costs.

Although double-stranded RNAs (e.g., double-stranded siRNAs) wereinitially thought to be required to initiate RNAi, several recentreports indicate that the antisense strand of such siRNAs is sufficientto initiate RNAi. Single-stranded antisense siRNAs can initiate RNAithrough the same pathway as double-stranded siRNAs (as evidenced, forexample, by the appearance of specific mRNA endonucleolytic cleavagefragments). As for double-stranded interfering RNAs, characteristics ofhigh-efficiency single-stranded siRNAs may vary by cell type (e.g., a 5′phosphate may be required on the antisense strand for efficientinduction of RNAi in some cell types, while a free 5′ hydroxyl issufficient in other cell types capable of phosphorylating the hydroxyl).See, e.g., Martinez et al. (2002) “Single-stranded antisense siRNAsguide target RNA cleavage in RNAi” Cell 110:563-574; Amarzguioui et al.(2003) “Tolerance for mutations and chemical modifications in a siRNA”Nucl. Acids Res. 31:589-595; Holen et al. (2003) “Similar behavior ofsingle-strand and double-strand siRNAs suggests that they act through acommon RNAi pathway” Nucl. Acids Res. 31:2401-2407; and Schwarz et al.(2002) Mol. Cell 10:537-548.

Due to differences in efficiency between siRNAs corresponding todifferent regions of a given target mRNA, several siRNAs are typicallydesigned and tested against the target mRNA to determine which siRNA ismost effective. Interfering RNAs can also be produced as small hairpinRNAs (shRNAs, also called short hairpin RNAs), which are processed inthe cell into siRNA-like molecules that initiate RNAi (see, e.g., Siolaset al. (2005) “Synthetic shRNAs as potent RNAi triggers” NatureBiotechnology 23:227-231).

The presence of RNA, particularly double-stranded RNA, in a cell canresult in inhibition of expression of a gene comprising a sequenceidentical or nearly identical to that of the RNA through mechanismsother than RNAi. For example, double-stranded RNAs that are partiallycomplementary to a target mRNA can repress translation of the mRNAwithout affecting its stability. As another example, double-strandedRNAs can induce histone methylation and heterochromatin formation,leading to transcriptional silencing of a gene comprising a sequenceidentical or nearly identical to that of the RNA (see, e.g., Schramkeand Allshire (2003) “Hairpin RNAs and retrotransposon LTRs effect RNAiand chromatin-based gene silencing” Science 301: 1069-1074; Kawasaki andTaira (2004) “Induction of DNA methylation and gene silencing by shortinterfering RNAs in human cells” Nature 431:211-217; and Morris et al.(2004) “Small interfering RNA-induced transcriptional gene silencing inhuman cells” Science 305: 1289-1292).

Short RNAs called microRNAs (miRNAs) have been identified in a varietyof species. Typically, these endogenous RNAs are each transcribed as along RNA and then processed to a pre-miRNA of approximately 60-75nucleotides that forms an imperfect hairpin (stem-loop) structure. Thepre-miRNA is typically then cleaved, e.g., by Dicer, to form the maturemiRNA. Mature miRNAs are typically approximately 21-25 nucleotides inlength, but can vary, e.g., from about 14 to about 25 or morenucleotides. Some, though not all, miRNAs have been shown to inhibittranslation of mRNAs bearing partially complementary sequences. SuchmiRNAs contain one or more internal mismatches to the corresponding mRNAthat are predicted to result in a bulge in the center of the duplexformed by the binding of the miRNA antisense strand to the mRNA. ThemiRNA typically forms approximately 14-17 Watson-Crick base pairs withthe mRNA; additional wobble base pairs can also be formed. In addition,short synthetic double-stranded RNAs (e.g., similar to siRNAs)containing central mismatches to the corresponding mRNA have been shownto repress translation (but not initiate degradation) of the mRNA. See,for example, Zeng et al. (2003) “MicroRNAs and small interfering RNAscan inhibit mRNA expression by similar mechanisms” Proc. Natl. Acad.Sci. USA 100:9779-9784; Doench et al. (2003) “siRNAs can function asmiRNAs” Genes & Dev. 17:438-442; Bartel and Bartel (2003) “MicroRNAs: Atthe root of plant development?” Plant Physiology 132:709-717; Schwarzand Zamore (2002) “Why do miRNAs live in the miRNP?” Genes & Dev. 16:1025˜1031; Tang et al. (2003) “A biochemical framework for RNA silencingin plants” Genes & Dev. 17:49-63; Meister et al. (2004)“Sequence-specific inhibition of microRNA- and siRNA-induced RNAsilencing” RNA 10:544-550; Nelson et al. (2003) “The microRNA world:Small is mighty” Trends Biochem. Sci. 28:534-540; Scacheri et al. (2004)“Short interfering RNAs can induce unexpected and divergent changes inthe levels of untargeted proteins in mammalian cells” Proc. Natl. Acad.Sci. USA 101:1892-1897; Sempere et al. (2004) “Expression profiling ofmammalian micro RNAs uncovers a subset of brain expressed microRNAs withpossible roles in murine and human neuronal differentiation” GenomeBiology 5:R13; Dykxhoom et al. (2003) “Killing the messenger: Short RNAsthat silence gene expression” Nature Reviews Molec. and Cell Biol.4:457-467; McManus (2003) “MicroRNAs and cancer” Semin Cancer Biol.13:253-288; and Stark et al. (2003) “Identification of DrosophilamicroRNA targets” PLoS Biol. 1:E60.

The cellular machinery involved in translational repression of mRNAs bypartially complementary RNAs (e.g., certain miRNAs) appears to partiallyoverlap that involved in RNAi, although, as noted, translation of themRNAs, not their stability, is affected and the mRNAs are typically notdegraded.

The location and/or size of the bulge(s) formed when the antisensestrand of the RNA binds the mRNA can affect the ability of the RNA torepress translation of the mRNA. Similarly, location and/or size of anybulges within the RNA itself can also affect efficiency of translationalrepression. See, e.g., the references above. Typically, translationalrepression is most effective when the antisense strand of the RNA iscomplementary to the 3′ untranslated region (3′ UTR) of the mRNA.Multiple repeats, e.g., tandem repeats, of the sequence complementary tothe antisense strand of the RNA can also provide more effectivetranslational repression; for example, some mRNAs that aretranslationally repressed by endogenous miRNAs contain 7-8 repeats ofthe miRNA binding sequence at their 3′ UTRs. It is worth noting thattranslational repression appears to be more dependent on concentrationof the RNA than RNA interference does; translational repression isthought to involve binding of a single mRNA by each repressing RNA,while RNAi is thought to involve cleavage of multiple copies of the mRNAby a single siRNA-RISC complex.

Guidance for design of a suitable RNA to repress translation of a giventarget mRNA can be found in the literature (e.g., the references aboveand Doench and Sharp (2004) “Specificity of microRNA target selection intranslational repression” Genes & Dev. 18:504-511; Rehmsmeier et al.(2004) “Fast and effective prediction of microRNA/target duplexes” RNA10:1507-1517; Robins et al. (2005) “Incorporating structure to predictmicro RNA targets” Proc Natl Acad Sci 102:4006-4009; and Mattick andMakunin (2005) “Small regulatory RNAs in mammals” Hum. Mol. Genet.14:R121-15 R132, among many others) and herein. However, due todifferences in efficiency of translational repression between RNAs ofdifferent structure (e.g., bulge size, sequence, and/or location) andRNAs corresponding to different regions of the target mRNA, several RNAsare optionally designed and tested against the target mRNA to determinewhich is most effective at repressing translation of the target mRNA.

Antibodies to Gene Products

An additional class of modulators are antibodies that bind to productsof genes linked to the loci herein. The antibodies can be utilized fordetecting and/or purifying the gene products e.g., in situ, to monitorthe gene product. Antibodies can also be used to block function of geneproducts, in vivo, in situ or in vitro. As used herein, the term“antibody” includes, but is not limited to, polyclonal antibodies,monoclonal antibodies, humanized or chimeric antibodies and biologicallyfunctional antibody fragments, which are those fragments sufficient forbinding of the antibody fragment to the protein.

For the production of antibodies to a relevant gene product, any of avariety of host animals may be immunized by injection with thepolypeptide, or a portion thereof. Such host animals may include, butare not limited to, rabbits, mice and rats, to name but a few. Variousadjuvants may be used to enhance the immunological response, dependingon the host species, including, but not limited to, Freund's (completeand incomplete), mineral gels such as aluminum hydroxide, surface activesubstances such as lysolecithin, pluronic polyols, polyanions, peptides,oil emulsions, keyhole limpet hemocyanin, dinitrophenol, and potentiallyuseful human adjuvants such as BCG (bacille Calmette-Guerin) andCorynebacterium parvum.

Polyclonal antibodies are heterogeneous populations of antibodymolecules derived from the sera of animals immunized with an antigen,such as target gene product, or an antigenic functional derivativethereof. For the production of polyclonal antibodies, host animals, suchas those described above, may be immunized by injection with the encodedprotein, or a portion thereof, supplemented with adjuvants as alsodescribed above.

Monoclonal antibodies (mAbs), which are homogeneous populations ofantibodies to a particular antigen, may be obtained by any techniquewhich provides for the production of antibody molecules by continuouscell lines in culture. These include, but are not limited to, thehybridoma technique of Kohler and Milstein (Nature 256:495-497, 1975;and U.S. Pat. No. 4,376,110), the human B-cell hybridoma technique(Kosbor et al., 20 Immunology Today 4:72, 1983; Cole et al., Proc.Nat'l. Acad. Sci. USA 80:2026-2030, 1983), and the EBV-hybridomatechnique (Cole et al., Monoclonal Antibodies and Cancer Therapy, AlanR. Liss, Inc., pp. 77-96, 1985). Such antibodies maybe of anyimmunoglobulin class, including IgG, IgM, IgE, IgA, IgD, and anysubclass thereof. The hybridoma producing the mAb of this invention maybe cultivated in vitro or in vivo. Production of high titers of mAbs invivo makes this the presently preferred method of production.

In addition, techniques developed for the production of “chimericmultibodies” (Morrison et al., Proc. Nat'l. Acad. Sci. USA 81:6851-6855,1984; Neuberger et al., Nature 312:604-608, 1984; Takeda et al., Nature314:452-454, 1985) by splicing the genes from a mouse antibody moleculeof appropriate antigen specificity, together with genes from a humanantibody molecule of appropriate biological activity, can be used. Achimeric antibody is a molecule in which different portions are derivedfrom different animal species, such as those having a variable orhypervariable region derived from a murine mAb and a humanimmunoglobulin constant region. Similarly, humanized antibodies can alsobe produced using available techniques.

Alternatively, techniques described for the production of single-chainantibodies (U.S. Pat. No. 4,946,778; Bird, Science 242:423-426, 1988;Huston et al., Proc. Nat'l. Acad. Sci. USA 85:5879-5883, 1988; and Wardet al., Nature 334:544-546, 10 1989) can be adapted to producedifferentially expressed gene-single chain antibodies. Single chainantibodies are fanned by linking the heavy and light chain fragments ofthe Fv region via an amino acid bridge, resulting in a single-chainpolypeptide.

In one aspect, techniques useful for the production of “humanizedantibodies” can be adapted to produce antibodies to the proteins,fragments or derivatives thereof. Such techniques are disclosed in U.S.Pat. Nos. 5,932,448; 5,693,762; 5,693,761; 5,585,089; 5,530,101;5,569,825; 5,625,126; 5,633,425; 5,789,650; 5,661,016; and 5,770,429.

Antibody fragments which recognize specific epitopes may be generated byknown techniques. For example, such fragments include, but are notlimited to, the F(ab′)₂ fragments, which can be produced by pepsindigestion of the antibody molecule, and the Fab fragments, which can begenerated by reducing the disulfide bridges of the F(ab′)₂ fragments.Alternatively, Fab expression libraries may be constructed (Huse et al.,Science 246:1275-1281, 1989) to allow rapid and easy identification ofmonoclonal Fab fragments with the desired specificity.

The protocols for detecting and measuring the expression of the geneproducts, using the above mentioned antibodies, are well known in theart. Such methods include, but are not limited to, dot blotting, westernblotting, competitive and noncompetitive protein binding assays,enzyme-linked immunosorbant assays (ELISA), immunohistochemistry,fluorescence-activated cell sorting (FACS), and others commonly used andwidely described in scientific and patent literature, and many employedcommercially.

One method, for ease of detection, is the sandwich ELISA, of which anumber of variations exist, all of which are intended to be encompassedby the present invention. For example, in a typical forward assay,unlabeled antibody is immobilized on a solid substrate and the sample tobe tested is brought into contact with the bound molecule and incubatedfor a period of time sufficient to allow formation of anantibody-antigen binary complex. At this point, a second antibody,labeled with a reporter molecule capable of inducing a detectablesignal, is then added and incubated, allowing time sufficient for theformation of a ternary complex of antibody-antigen-labeled antibody. Anyunreacted material is washed away, and the presence of the antigen isdetermined by observation of a signal, or may be quantitated bycomparing with a control sample containing known amounts of antigen.Variations on the forward assay include the simultaneous assay, in whichboth sample and antibody are added simultaneously to the bound antibody,or a reverse assay, in which the labeled antibody and sample to betested are first combined, incubated and added to the unlabeled surfacebound antibody. These techniques are well known to those skilled in theart, and the possibility of minor variations will be readily apparent.As used herein, “sandwich assay” is intended to encompass all variationson the basic two-site technique. For the immunoassays of the presentinvention, the only limiting factor is that the labeled antibody be anantibody which is specific for the protein expressed by the gene ofinterest.

The most commonly used reporter molecules in this type of assay areeither enzymes, fluorophore- or radionuclide-containing molecules. Inthe case of an enzyme immunoassay, an enzyme is conjugated to the secondantibody, usually by means of glutaraldehyde or periodate. As will bereadily recognized, however, a wide variety of different ligationtechniques exist which are well-known to the skilled artisan. Commonlyused enzymes include horseradish peroxidase, glucose oxidase,beta-galactosidase and alkaline phosphatase, among others. Thesubstrates to be used with the specific enzymes are generally chosen forthe production, upon hydrolysis by the corresponding enzyme, of adetectable color change. For example, p-nitrophenyl phosphate issuitable for use with alkaline phosphatase conjugates; for peroxidaseconjugates, 1,2-phenylenediamine or toluidine are commonly used. It isalso possible to employ fluorogenic substrates, which yield afluorescent product, rather than the chromogenic substrates noted above.A solution containing the appropriate substrate is then added to thetertiary complex. The substrate reacts with the enzyme linked to thesecond antibody, giving a qualitative visual signal, which may befurther quantitated, usually spectrophotometrically, to give anevaluation of the amount of PLAB which is present in the serum sample.

Alternately, fluorescent compounds, such as fluorescein and rhodamine,can be chemically coupled to antibodies without altering their bindingcapacity. When activated by illumination with light of a particularwavelength, the fluorochrome-labeled antibody absorbs the light energy,inducing a state of excitability in the molecule, followed by emissionof the light at a characteristic longer wavelength. The emission appearsas a characteristic color visually detectable with a light microscope.Immunofluorescence and EIA techniques are both very well established inthe art and are particularly preferred for the present method. However,other reporter molecules, such as radioisotopes, chemiluminescent orbioluminescent molecules may also be employed. It will be readilyapparent to the skilled artisan how to vary the procedure to suit therequired use.

Cell Rescue and Therapeutic Administration

In one aspect, the invention includes rescue of a cell that is defectivein function of one or more endogenous genes or polypeptides of FIGS. 1and/or 2 (thus conferring the relevant phenotype of interest, e.g.,breast cancer susceptibility, resistance, etc.). This can beaccomplished simply by introducing a new copy of the gene (or aheterologous nucleic acid that expresses the relevant protein), i.e., agene having an allele that is desired, into the cell. Other approaches,such as homologous recombination to repair the defective gene (e.g., viachimeraplasty) can also be performed. In any event, rescue of functioncan be measured, e.g., in any of the assays noted herein. Indeed, thismethod can be used as a general method of screening cells in vitro forexpression or activity of any gene or gene product of FIGS. 1 and/or 2.Accordingly, in vitro rescue of function is useful in this context forthe myriad in vitro screening methods noted above. The cells that arerescued can include cells in culture, (including primary or secondarycell culture from patients, as well as cultures of well-establishedcells). Where the cells are isolated from a patient, this has additionaldiagnostic utility in establishing which gene or product is defective ina patient that presents with a relevant phenotype.

In another aspect, the cell rescue occurs in a patient, e.g., a human,e.g., to remedy a defect. Thus, one aspect of the invention is genetherapy to remedy defects. In these applications, the nucleic acids ofthe invention are optionally cloned into appropriate gene therapyvectors (and/or are simply delivered as naked or liposome-conjugatednucleic acids), which are then delivered, optionally in combination withappropriate carriers or delivery agents. Proteins can also be delivereddirectly, but delivery of the nucleic acid is typically preferred inapplications where stable expression is desired. Similarly, modulatorsof any defect identified by the methods herein can be usedtherapeutically.

Compositions for administration, e.g., comprise a therapeuticallyeffective amount of the modulator, gene therapy vector or other relevantnucleic acid, and a pharmaceutically acceptable carrier or excipient.Such a carrier or excipient includes, but is not limited to, saline,buffered saline, dextrose, water, glycerol, ethanol, and/or combinationsthereof. The formulation is made to suit the mode of administration. Ingeneral, methods of administering gene therapy vectors for topical useare well known in the art and can be applied to administration of thenucleic acids of the invention.

Therapeutic compositions comprising one or more modulator or genetherapy nucleic acid of the invention are optionally tested in one ormore appropriate in vitro and/or in vivo animal model of disease, toconfirm efficacy, tissue metabolism, and to estimate dosages, accordingto methods well known in the art. In particular, dosages can initiallybe determined by activity, stability or other suitable measures of theformulation.

Administration is by any of the routes normally used for introducing amolecule into ultimate contact with cells. Modulators and/or nucleicacids that encode a relevant sequence can be administered in anysuitable manner, optionally with one or more pharmaceutically acceptablecarriers. Suitable methods of administering such nucleic acids in thecontext of the present invention to a patient are available, and,although more than one route can be used to administer a particularcomposition, a particular route can often provide a more immediate andmore effective action or reaction than another route.

Pharmaceutically acceptable carriers are determined in part by theparticular composition being administered, as well as by the particularmethod used to administer the composition. Accordingly, there is a widevariety of suitable formulations of pharmaceutical compositions of thepresent invention. Compositions can be administered by a number ofroutes including, but not limited to: oral, intravenous,intraperitoneal, intramuscular, transdermal, subcutaneous, topical,sublingual, or rectal administration. Compositions can be administeredvia liposomes (e.g., topically), or via topical delivery of naked DNA orviral vectors. Such administration routes and appropriate formulationsare generally known to those of skill in the art.

The compositions, alone or in combination with other suitablecomponents, can also be made into aerosol formulations (i.e., they canbe “nebulized”) to be administered via inhalation. Aerosol formulationscan be placed into pressurized acceptable propellants, such asdichlorodifluoromethane, propane, nitrogen, and the like. Formulationssuitable for parenteral administration, such as, for example, byintraarticular (in the joints), intravenous, intramuscular, intradermal,intraperitoneal, and subcutaneous routes, include aqueous andnon-aqueous, isotonic sterile injection solutions, which can containantioxidants, buffers, bacteriostats, and solutes that render theformulation isotonic with the blood of the intended recipient, andaqueous and non-aqueous sterile suspensions that can include suspendingagents, solubilizers, thickening agents, stabilizers, and preservatives.The formulations of packaged nucleic acid can be presented in unit-doseor multi-dose sealed containers, such as ampules and vials.

The dose administered to a patient, in the context of the presentinvention, is sufficient to effect a beneficial therapeutic response inthe patient over time. The dose is determined by the efficacy of theparticular vector, or other formulation, and the activity, stability orserum half-life of the polypeptide which is expressed, and the conditionof the patient, as well as the body weight or surface area of thepatient to be treated. The size of the dose is also determined by theexistence, nature, and extent of any adverse side-effects that accompanythe administration of a particular vector, formulation, or the like in aparticular patient. In determining the effective amount of the vector orformulation to be administered in the treatment of disease, thephysician evaluates local expression, or circulating plasma levels,formulation toxicities, progression of the relevant disease, and/orwhere relevant, the production of antibodies to proteins encoded by thepolynucleotides. The dose administered, e.g., to a 70 kilogram patientare typically in the range equivalent to dosages of currently-usedtherapeutic proteins, adjusted for the altered activity or serumhalf-life of the relevant composition. The vectors of this invention cansupplement treatment conditions by any known conventional therapy.

For administration, formulations of the present invention areadministered at a rate determined by the LD-50 of the relevantformulation, and/or observation of any side effects of the vectors ofthe invention at various concentrations, e.g., as applied to the mass ortopical delivery area and overall health of the patient. Administrationcan be accomplished via single or divided doses.

If a patient undergoing treatment develops fevers, chills, or muscleaches, he/she receives the appropriate dose of aspirin, ibuprofen,acetaminophen or other pain/fever controlling drug. Patients whoexperience reactions to the compositions, such as fever, muscle aches,and chills are premedicated 30 minutes prior to the future infusionswith either aspirin, acetaminophen, or, e.g., diphenhydramine.Meperidine is used for more severe chills and muscle aches that do notquickly respond to antipyretics and antihistamines. Treatment is slowedor discontinued depending upon the severity of the reaction.

Diagnostic and Prognostic Assays

The nucleic acids, polypeptides, antibodies and other compositionsherein may be utilized as reagents (e.g., in pre-packaged kits) forprognosis and diagnosis of susceptibility or resistance to breast cancerphenotypes. The methods can be practiced on subjects known to have oneor more symptoms of a breast cancer phenotype as part of a differentialdiagnosis or prognosis of other diseases. The methods can also bepracticed on subjects having a known susceptibility to a breast cancerphenotype. The polymorphic profile of such an individual can increase ordecrease the assessment of susceptibility. For example, an individualhaving two siblings with breast cancer is known to be at increasedsusceptibility to the disease compared with the general population. Afinding of additional factors favoring susceptibility increases the riskwhereas finding factors favoring resistance decreases the risk.

The invention provides methods of determining the polymorphic profile ofan individual at one or more of SNPs of the invention. The SNPs includesthose shown in FIGS. 1 and 2, and those in linkage disequilibrium withthem. Those in linkage disequilibrium with them usually occur in thesame genes or within 100 or 50 or 20 kb of the same genes. SNPs inlinkage disequilibrium with the SNPs in the Figures herein can bedetermined by haplotype mapping. Haplotypes can be determined by fusingdiploid cells from different species. The resulting cells are partiallyhaploid, allowing determination of haplotypes on haploid chromosomes(see, e.g., US 20030099964). Alternatively, SNPs in linkagedisequilibrium with exemplified SNPs can be determined by similarassociation studies to those described in the examples below.

The polymorphic profile constitutes the polymorphic forms occupying thevarious polymorphic sites in an individual. In a diploid genome, twopolymorphic forms, the same or different from each other, usually occupyeach polymorphic site. Thus, the polymorphic profile at sites X and Ycan be represented in the form X (x1, x1), and Y (y1, y2), wherein x1,x1 represents two copies of allele x1 occupying site X and y1, y2represent heterozygous alleles occupying site Y.

The polymorphic profile of an individual can be scored by comparisonwith the polymorphic forms associated with resistance or susceptibilityto breast cancer phenotypes occurring at each site as shown in theFigures herein. The comparison can be performed on at least, e.g., 1, 2,5, 10, 25, 50, or all of the polymorphic sites, and optionally, othersin linkage disequilibrium with them. The polymorphic sites can beanalyzed in combination with other polymorphic sites. However, the totalnumber of polymorphic sites analyzed is usually fewer than 10,000, 1000,100, 50 or 25 and can be about 10 or less, about 5 or less, or about 2or less.

The number of resistance or susceptibility alleles present in aparticular individual can be combined additively or as ratio to providean overall score for the individual's genetic propensity to breastcancer phenotypes (see U.S. Ser. No. 60/566,302, filed Apr. 28, 2004,U.S. Ser. No. 60/590,534, filed Jul. 22, 2004, U.S. Ser. No. 10/956,224filed Sep. 30, 2004, and PCT US05/07375 filed Mar. 3, 2005). Resistancealleles can be arbitrarily each scored as +1 and susceptibility allelesas −1 (or vice versa). For example, if an individual is typed at 100polymorphic sites of the invention and is homozygous for resistance atall of them, he could be assigned a score of 100% genetic propensity toresistance to breast cancer phenotypes or 0% propensity tosusceptibility to breast cancer phenotypes. The reverse applies if theindividual is homozygous for all susceptibility alleles. More typically,an individual is homozygous for resistance alleles at some loci,homozygous for susceptibility alleles at some loci, and heterozygous forresistance/susceptibility alleles at other loci. Such an individual'sgenetic propensity for breast cancer phenotypes can be scored byassigning all resistance alleles a score of +1, and all susceptibilityalleles a score of −1 (or vice versa) and combining the scores. Forexample, if an individual has 102 resistance alleles and 204susceptibility alleles, the individual can be scored as having a 33%genetic propensity to resistance and 67% genetic propensity tosusceptibility. Alternatively, homozygous resistance alleles can beassigned a score of +1, heterozygous alleles a score of zero andhomozygous susceptibility alleles a score of −1. The relative numbers ofresistance alleles and susceptibility alleles can also be expressed as apercentage. Thus, an individual who is homozygous for resistance allelesat 30 polymorphic sites, homozygous for susceptibility alleles at 60polymorphic sites, and heterozygous at the remaining 63 sites isassigned a genetic propensity of 33% for resistance. As a furtheralternative, homozygosity for susceptibility can be scored as +2,heterozygosity, as +1 and homozygosity for resistance as 0.

The individual's score, and the nature of the polymorphic profile areuseful in prognosis or diagnosis of an individual's susceptibility tobreast cancer phenotypes. Optionally, a patient can be informed ofsusceptibility to a breast cancer phenotype indicated by the geneticprofile. Presence of a high genetic propensity to breast cancerphenotypes can be treated as a warning to commence prophylactic ortherapeutic treatment. For example, individuals with elevated risk ofdeveloping a breast cancer phenotype may be monitored differently (e.g.,more frequent mammography) or may be treated prophylactically (e.g.,with one or more drugs). Presence of a high propensity to a breastcancer phenotype also indicates the utility of performing secondarytesting, such as a biopsy.

Polymorphic profiling is useful, for example, in selecting agents toeffect treatment or prophylaxis of breast cancer phenotypes in a givenindividual. Individuals having similar polymorphic profiles are likelyto respond to agents in a similar way.

Polymorphic profiling is also useful for stratifying individuals inclinical trials of agents being tested for capacity to treat breastcancer phenotypes or related conditions. Such trials are performed ontreated, or control populations having similar or identical polymorphicprofiles (see EP99965095.5), for example, a polymorphic profileindicating an individual has an increased risk of developing a breastcancer phenotype. Use of genetically matched populations eliminates orreduces variation in treatment outcome due to genetic factors, leadingto a more accurate assessment of the efficacy of a potential drug.Computer-implemented algorithms can be used to identify more geneticallyhomogenous subpopulations in which treatment or prophylaxis has asignificant effect notwithstanding that the treatment or prophylaxis isineffective in more heterogeneous larger populations. In such methods,data are provided for a first population with a breast cancer phenotypetreated with an agent, and a second population also with the breastcancer phenotype but treated with a placebo. The polymorphic profile ofindividuals in the two populations is determined in at least onepolymorphic site in or within 100 kb or 50 kb or 20 kb of a geneselected from those shown in FIGS. 1 and/or 2. Data are also provided asto whether each patient in the populations reaches a desired endpointindicative of successful treatment or prophylaxis. Subpopulations ofeach of the first and second populations are then selected such that theindividuals in the subpopulations have greater similarity of polymorphicprofiles with each other than do the individuals in the original firstand second populations. There are many criteria by which similarity canbe assessed. For example, one criterion is to require that individualsin the subpopulations have at least one susceptibility allele at each ofat least ten of the above genes. Another criterion is that individualsin the subpopulations have at least 75% susceptibility alleles for eachof the polymorphic sites at which the polymorphic profile is determined.Regardless of the criteria used to assess similarity, the endpoint dataof the subpopulations are compared to determine whether treatment orprophylaxis has achieved a statistically significant result in thesubpopulations. As a result of computer implementation, billions ofcriteria for similarity can be analyzed to identify one or a fewsubpopulations showing statistical significance.

Polymorphic profiling is also useful for excluding individuals with nopredisposition to breast cancer phenotypes from clinical trials.Including such individuals in the trial increases the size of thepopulation needed to achieve a statistically significant result.Individuals with no predisposition to breast cancer phenotypes can beidentified by determining the numbers of resistances and susceptibilityalleles in a polymorphic profile as described above. For example, if asubject is genotyped at ten sites in ten genes of the inventionassociated with breast cancer phenotypes, twenty alleles are determinedin total. If over 50% and preferably over 60% or 75% percent of theseare resistance genes, the individual is unlikely to develop a breastcancer phenotype and can be excluded from the trial.

In other embodiments, stratifying individuals in clinical trials may beaccomplished using polymorphic profiling in combination with otherstratification methods, including, but not limited to, family history,risk models (e.g., Gail Score, Claus model), clinical phenotypes (e.g.,atypical lesions and breast density), and specific candidate biomarkers(e.g., IGF1, IFG2, IGFBP3, Ki-67, and estradiol). For example,stratification of higher risk in chemoprevention trials that includesstratification based on polymorphic profiles can improve outcomes. Inparticular, markers linked to FGFR2 can be used to stratify anti-VEGF oranti-angiogenesis therapy response, and markers linked to PKHD1 can beused to stratify anti-EGF therapy efficacy (anti-EGF therapies areactive in patients with polycystic kidney and hepatic disease).

Polymorphic profiles can also be used after the completion of a clinicaltrial to elucidated differences in response to a given treatment. Forexample, the set of polymorphisms can be used to stratify the enrolledpatients into disease sub-types or classes. It is also possible to usethe polymorphisms to identify subsets of patients with similarpolymorphic profiles who have unusual (high or low) response totreatment or who do not respond at all (non-responders). In this way,information about the underlying genetic factors influencing response totreatment can be used in many aspects of the development of treatment(these range from the identification of new targets, through the designof new trials to product labeling and patient targeting). Additionally,the polymorphisms can be used to identify the genetic factors involvedin adverse response to treatment (adverse events). For example, patientswho show adverse response may have more similar polymorphic profilesthan would be expected by chance. This allows the early identificationand exclusion of such individuals from treatment. It also providesinformation that can be used to understand the biological causes ofadverse events and to modify the treatment to avoid such outcomes.

Polymorphic profiles can also be used for other purposes, includingpaternity testing and forensic analysis as described by U.S. Pat. No.6,525,185. In forensic analysis, the polymorphic profile from a sampleat the scene of a crime is compared with that of a suspect. A matchbetween the two is evidence that the suspect in fact committed thecrime, whereas lack of a match excludes the suspect. The presentpolymorphic sites can be used in such methods, as can other polymorphicsites in the human genome.

EXAMPLES

The following examples are offered to illustrate, but not to limit theclaimed invention. One of skill will recognize a variety of non-criticalparameters that can be altered within the scope of the invention.

Example 1 Strategies for Identification of Breast Cancer MarkersIntroduction: Identifying Common Genetic Variants

There are important applications to public health in the identificationof breast cancer marker alleles. Where genetic variation is due to manyloci, risks to individuals vary widely, depending upon the number ofhigh-risk alleles inherited at susceptibility loci. Our analyses basedon the model of Antoniou et al¹³ suggest that there may be as much as40-fold difference in risk between the top and bottom 20% of the 10population. Under the same model, half of all breast cancers occur inthe 12% of women at greatest risk, and these women have risks of atleast 1 in 8 by age 70. By contrast, the 50% of women at least risk haveonly 12% of the cancers, and individual risks of less than 1 in 30¹⁴.Genes that are identified as being correlated to breast cancer risk canbe used for estimation of associated and individual risks. The practicalconsequences of this risk estimation are substantial.

Common genetic variants that confer modest degrees of risk haveindividually important effects at the population level. For example, acommon variant, with frequency 20%, which increases individual risk byonly 1.5-fold would account for 15% of the population burden of acancer. The analogy is with moderate elevations of blood pressure, or ofcholesterol, in cardiovascular disease. If the variant indicates afeasible mechanism for intervention, this also provides novelpossibilities for targeted prevention.

In addition to these practical outcomes, the identification of cancersusceptibility genes helps to clarify mechanisms of carcinogenesis (ashas already happened, for example, with BRCA1 and BRCA2). Extendingbeyond known candidates to a whole genome search has the great advantagethat totally novel mechanisms emerge. These mechanisms also provide newtherapeutic targets.

Finally, knowledge of susceptibility genes allows us to clarify theeffects of lifestyle risk factors by studying the effects of genes andthese risk factors in combination, using for example the EPIC cohort.

Breast Cancer

Although arguments may be made for association studies in many cancers,there are several reasons why it is particularly appropriate to carryout a study in breast cancer. It is the commonest cancer in women, andits aetiology is still poorly understood. The genetic basis for thedisease has been more thoroughly investigated than for any other commoncancer. As a result, the evidence in favor of a polygenic basis isclearer than for other cancers. Long-term studies have assembledsufficiently large series of cases to identify susceptibility locireliably. In addition, cases with a strong family history are availablethrough cancer genetics clinics and can provide substantial gains inefficiency in the association study (see ‘Research Proposal’). Finally,there are interventions that can be offered to women found to be atincreased risk. For example, prophylactic oophorectomy can reducesubstantially the subsequent risk of breast cancer¹⁵. Recent studiessuggest that screening by MRI may provide much greater sensitivity thanmammography but at significantly greater cost¹⁶.

Study Design

Genotypes for 200,000 single nucleotide polymorphisms (SNPs) aredetermined in a set of 400 familial breast cancer cases and 400 controlsfrom the EPIC cohort; 5% of these SNPs showing the strongest associationare analyzed in further population-based series of 4,600 cases and 4,600controls. Positive associations at this stage are confirmed in furtherlarge case-control series.

In addition to the breast cancer endpoint, many quantitative phenotypesare available in the control set and provide additional data for geneticanalysis. These include phenotypes (e.g. mammographic patterns, hormonelevels) that are related to cancer risk.

Yield

The scan evaluates single nucleotide polymorphisms of frequency 10% orgreater (and some in the 5-10% range) across the entire genome outsiderepetitive sequences. It has approximately 80% power to detect anycommon variant within these regions that accounts for 2% or more of theoverall inherited component of breast cancer.

The Design of Studies to Search for Common Susceptibility Variants

An efficient design to identify common low risk alleles is acase/control study. Variants that are associated with susceptibility areidentified by their occurrence at a significantly higher frequency incancer cases than in controls matched for genetic background. In thisstudy, the variants are single nucleotide polymorphisms (SNPs). Mostoften, the active or functional variant that might be relevant todisease susceptibility is not known, and so the search relies on a setof ‘tagging’ SNPs that can report on the presumed (but unknown) activevariants.

The case-control association study approach has already been usedextensively in breast cancer on a “candidate gene” basis. Polymorphismsin the coding region and intrans of close to 100 genes have previouslybeen studied in this way. These include, for example, genes involved insex-steroid hormone metabolism, cell-cycle control and DNA repair.Although some associations have been suggested for common variants, nonehas been definitively established. The results to date suggest that themajority of the variation in breast cancer risk is not due to variantsin the intragenic DNA of the genes that would be a first choice asbreast cancer candidates. There are, moreover, serious limitations to acandidate gene approach. It is slow and relatively expensive, beingdependent on developing assays on a SNP by SNP basis for each gene to betested; it is incomplete in its coverage even of the candidate genes, inparticular ignoring, in most cases, potential regulatory variation; andit is restricted by current knowledge of the biology of the disease. Agenome-wide search, by contrast, has the potential to identify activecommon variants without any prior knowledge of function or location.

Genome Scanning SNPs

A requirement for a genome scan is to define a set of SNPs that providesthe best compromise between completeness and cost in reporting on theset of all other SNPS across the genome. Perlegen Sciences(www(dot)perlegen(dot)com) have identified 1.1 million common SNPmarkers (a density of 1 SNP per 2 kb) by resequencing the nonrepetitivesequences of the human genome in 20 to 50 haploid genomes segregated inhuman/rodent somatic cell hybrids. This SNP search is based on a similarstrategy to that reported in a study of chromosome 21 reported by Patilet al¹⁷. From this they have defined, using a dynamic programmingalgorithm¹⁸, a set of 200,000 tagging SNPs that report unambiguouslymore than 80% of common haplotypes defined by the complete set of 1.1million SNPs. It is this set of 200,000 tagging SNPs that were used inthis example.

The SNPs are typed on high-density oligonucleotide arrays developed byAffymetrix, which have been extensively validated in routine use.Briefly, the array design uses 80 features (25-mer oligonucleotides) toquery each SNP. The 80 features comprise 10 overlapping feature setswhere each feature set includes 4 features specific for the referenceallele (one perfect match and 3 mismatch features) and 4 similarfeatures for the alternative allele. By comparing the fluorescenceintensities of perfect match features for the reference allele withthose that are perfect matches for the alternative allele, the threepossible SNP genotypes (common homozygote, heterozygote and rarehomozygote) can be distinguished. To carry out the genotyping assay,regions of the sample genome containing SNPs of interest arespecifically amplified using multiplex (78-plex) short range PCR. ThePCR products from each individual are pooled and labeled with biotin tocreate target DNA. The target DNA is hybridized to the SNP-typing highdensity oligonucleotide arrays. After overnight hybridization, thearrays are washed, stained and scanned for fluorescence intensities.

In this example, the features to genotype the 200,000 SNPs are arrayedonto a series of 6 high-density arrays, requiring that target DNA with acomplexity of approximately 30,000 SNPs be used for hybridization. Atarget of this complexity gives a call rate of 97.3%. Comparison of thehigh density array genotyping technology with other technologies(real-time PCR and fluorescence polarization) shows a consistentconcordance of greater than 99% in approximately 20,000 genotypings withup to 20 different SNPs. The technology has proven to be robust whenused with DNA from a variety of collaborating clinical and researchlaboratories, and to work well with genome amplified DNA.

A property of the 200,000 tagging SNPs to be used in this study, istheir ability to ‘report’ on all other SNP variants within the genome.For given power, the required sample size is proportional to 1/r², wherer is the coefficient of linkage disequilibrium between the functionalvariant which is being sought and the most closely linked tagging SNP¹⁹.

The distribution of r² between non-tagging SNPs and their correspondingtagging SNP was determined empirically by genotyping 1608 SNPs, evenlyspaced over a 4 Mb region of genomic DNA, in 28 unrelated individuals(56 chromosomes): see Table 1. The mean r² for all 988 tester SNPs, eachwith a minor allele frequency of >10%, was 67%, with 69% of SNPs havingan r² greater than 0.5.

Table 1

Table 1 Distribution of r² values between 417 selected ‘tagging’ SNPsand 988 ‘tester’ SNPs, determined in a 4 Mb segment of chromosome 21 in28 individuals distinct from those used for SNP discovery. 15% of thetotal set of SNPs had minor allele frequencies 1-10%; 85% hadfrequencies greater than 10% with an even distribution between 10 and50%. All tester SNPs had a minor allele frequency>10%. The averagespacing of the 417 tagging SNP set was 1 per 10 kb, similar to that inthe 200,000 SNP set to be used in the genome scan.

TABLE 1 r² % of tester SNPs 0.9-1.0  34% 0.8-0.89 10% 0.7-0.79  9%0.6-0.69  9% 0.5-0.59  8% 0.4-0.49  6% 0.3-0.39  7% 0.2-0.29  7%0.1-0.19  8% 0.0-0.09  2%

Increasing the set of 200,000 tagging SNPs increases the proportion ofSNPs in the total genome that are reported, but at increased cost. Evena set of 1.1 million SNPs would not provide complete coverage, sincesome bases could not be assayed and some common SNPs are missed due tothe limited number of chromosomes surveyed. We conclude that the 200,000tagging SNP set provides a good compromise between coverage and cost.

Previous studies focus on the genetics of cancer predisposition,including an increasing focus on low penetrancesusceptibility^(13,14,20-23). Relevant topics for include: (1) assemblyof case and control sets; (2) development of genetic models for breastcancer susceptibility; (3) establishment of laboratory facilities forassociation studies.

(1) Sample Sets

Breast cancer cases—population based set. We have assembled a populationbased set of (currently 4900) cases of invasive breast cancer diagnosedbefore the age of 70, ascertained through the local Anglian CancerRegistry. The median time 15 from diagnosis to completion of recruitmentis 6 months (interquartile range 3 to 9 months). 65% of all eligiblecases have provided a blood sample. This set provides some of thefamilial cases to be analyzed in stage 1 of our study, and thepopulation based series of cases for stage 2. In addition to a bloodsample, subjects complete a questionnaire which includes family historyto second degree relatives, reproductive history, breast feeding, oralcontraceptive and HRT use, benign breast disease, medical historyincluding other cancers, smoking, alcohol, education and ethnic group.Registry data include clinical stage, pathological grade and stage,simple treatment data and follow-up for survival. Paraffin blocks oftumour are available from 800 cases currently, and can in principle becollected for the majority of the entire set if funding is available.

Breast cancer cases—familial set. Through the familial breast cancerclinic in Cambridge and the population-based set described above, a setof over 200 cases with either a strong family history of breast canceror bilateral primary breast cancers has been assembled, that have testednegative for BRCA1 and BRCA2 mutations. These cases, together withsimilar cases obtained by collaboration with other CR UK groups, formsthe ‘genetically enriched’ case set for the first stage of theassociation study.

Controls. Control DNAs for both stage 1 and stage 2 of the study areobtained from the EPIC-Norfolk cohort²⁴. This is part of the MulticentreEuropean Prospective Investigation of Cancer, a 450,000 strongpopulation based cohort of men and women aged 45 to 70 at recruitmentfrom whom blood, extensive epidemiological information and follow up areavailable. The 25,000 participants in EPIC-Norfolk are volunteersascertained from family medical practices in Norfolk, which is withinthe same Anglian region from which the breast cancer cases are obtained.In addition to providing the controls for the gene discovery phase ofthis project, the larger EPIC cohort provides samples and data forconfirmation of positive associations and for the investigation ofgene/lifestyle interactions at the follow-up stage.

The study population is relatively homogeneous ethnically, with morethan 95% of the population recorded as white and born in the U.K.Evidence for population stratification in this population has beenevaluated by genotyping 1655 controls for SNPs in 23 unlinked genes. Nosignificant association between unlinked loci was found, indicating noevidence of stratification²⁵.

Additional phenotypic information in the EPIC control set. Of relevanceto the study, extensive phenotypic information is either available (insubsets of individuals) or can readily be obtained, from the 400 EPICcontrols who will be genotyped for 200,000 SNPs in stage 1. Thesequantitative or semi-quantitative phenotypes are evaluated for genotypeassociations. Phenotypes relevant to breast cancer include: mammographicdensity, heel bone density, body mass index, and a range of measurementsin serum, of which so far estrogen metabolites, SHBG, IGF-1, and somecytokines are already available in different sets of individuals. Otherphenotypes include blood pressure, lipid profiles, C-reactive protein,fibrinogen, full blood count, glycated haemoglobin and thyroid function.In 2004 and 2005 limited recalls are planned for re-interview andfurther blood sampling, with the possibility of additional phenotypingand the collection of fresh serum and viable cells.

(2) Genetic Models for Breast Cancer Susceptibility.

We analysed the first 1500 breast cancers ascertained in the Anglianpopulation-based study for mutations in BRCA1 and BRCA2, and found,consistent with Peto et al, that only 15% of the familial clustering ofbreast cancer is attributable to mutations in these genes. Oursegregation analysis of the patterns of breast cancer in the families ofcases in this study (subsequently tested on other series) led to thepolygenic model summarised earlier¹³. This model in turn underlies thecalculations of the increased power for association studies provided byusing familial rather than unselected cases, which is the basis of theproposed two-stage design used in this example²⁶.

(3) Laboratory Set Up for Sample Processing and SNP Genotyping.

A moderate throughput genotyping laboratory based on the 384-well Taqmanplatform, is used for candidate gene association studies. Genotypingcapacity is ˜100,000 SNPs per week.

In brief, the laboratory set up is as follows. Study participants aregiven a code-number at recruitment which remains attached to all theirdata and their biological sample tubes as a bar-code. Within thelaboratory, samples are tracked with a Laboratory Information ManagementSystem (Thermo, Altringham UK). DNA is extracted, in batches of 96subjects, from whole blood in coded tubes by Whatman Ltd (Ely, UK) andreturned in coded arrays with DNA normalised to 40 ng/μl.Pre-amplification of the whole genome is performed on the normalisedarrays and the products stored in aliquots. 384-well working-stocks forgenotyping are created from equal numbers of cases and controlsinterleaved with blank wells as negative controls. 3% of samples from astudy are duplicated. Thus, the cases and controls (described above) areheld in 13 plates—12 of unique samples and a 13^(th) of duplicates.Genotyping is carried out on all study-plates simultaneously—reagentsare added by robot (Matrix, UK), thermal cycling on MJ Tetrads (GRI, UK)and end-point fluorescence detection by 7900 Sequence Detector (ABI,Warrington, UK). Genotypes are exported to a database and linked to thephenotypic data on each subject. Control genotypes are tested fordeparture from Hardy-Weinberg Equilibrium as a final quality controlstep.

Research Design

The study is organised in stages:

Stage 1. The full set of 200,000 tagging SNPs is analysed in 400unrelated breast cancer cases enriched for family history, and 400female controls drawn from the EPIC study. The breast cancer cases willhave been screened negative for BRCA1/2 mutations.

Stage 2. SNPs that show a significant difference in frequency betweenthe cancer series and the control series, at the p<0.05 level, arere-evaluated in a further 4600 breast cancer cases and 4600 matchedcontrols.

Rationale for the Research Design

The staged design is chosen to minimise the amount of genotypingrequired, while retaining a high power to detect SNPs with a modesteffect on risk. With the proposed thresholds, approximately 10,000 SNPswill go forward to stage 2, while substantially fewer (depending on thenumber of “true” associations) are expected to be put forward at the endof stage 2 for additional verification in other studies. Calculationshave shown that such a staged design is very efficient compared withgenotyping all samples for all SNPs²⁷.

Cases—Stage 1

Cases are women with invasive breast cancer with at least two firstdegree relatives with breast cancer, or equivalently strong familyhistory (for example, one first and two second degree relativesaffected). These women are selected from cancer genetics centres in theU.K. or from the Anglian Breast Cancer Study. Women whose ethnic groupis not recorded as white will be excluded.

We have previously demonstrated that the power to detect associations isstrongly related to the degree of family history of the cases²⁶. The useof cases with two affected first degree relatives reduces the requiredsample size by at least fourfold, as compared with using unselectedcases. From amongst all available cases, we will select the four hundredcases with the strongest family history. If more than one case isavailable from the same family we will choose the case with thestrongest immediate family history, so that all cases in the set will beunrelated.

All cases are screened (and are negative) for mutations in BRCA1 andBRCA2. This screening includes, screening of all exons and splicejunctions by a sensitive screening technique (e.g. CSGE). This is donebecause it is unknown whether low penetrance alleles that influencebreast cancer risk in non-carriers of BRCA1 or BRCA2 mutations will alsoinfluence the risk in carriers. The analysis of Antoniou et al¹³suggests a similar “polygenic” component in carriers. However, it ispossible that genes modifying the risk in BRCA1 and BRCA2 carriers maybe different, particularly given the distinctive pathology of BRCA1tumours. BRCA1 and BRCA2 mutations would be present in more than 20% ofcases selected by the criteria used in stage 1. If a polymorphism ofinterest did not influence the disease risk in carriers, inclusion ofcarriers could reduce the power of the study. The study, thus,conservatively screens for and excludes known BRCA1 and BRCA2 mutationcarriers. This approach is estimated to exclude approximately 70% ofBRCA1 mutations and 90% of BRCA2 mutations, so that less than 5% ofcases in the final set are likely to harbour unidentified mutations.

Cases—Stage 2

Cases at stage 2 consist of 4,600 cases drawn from the population-basedAnglian Breast Cancer (ABC) Study.

While there is an argument for the use of “enriched” cases to maximizepower and minimise costs at stage 1, the case is more finely balanced atstage 2. Use of familial cases increases power, but the gain is lessmarked because the main determinant of power is the efficiency ofstage 1. At the same time, the population-based case-control sets arealready in use for candidate gene association studies, and DNA samplesare already arrayed from stage 1. Developing a new set of familial caseson this scale would entail considerable delay and expense. Secondly, thecases are closely matched geographically to the controls, providing moreprotection against false positive associations due to regional variationin allele frequencies. Thirdly, the population-based series provides adirect estimate of the relative risk associated with each SNP orhaplotype. Fourthly, the ABC study has collected systematicallyinformation on lifestyle risk factors and clinical outcome of thecancers. This provides the potential for further analyses to studyassociations with survival and interactions with lifestyle risk factors.The same quality of information could not be obtained on familial cases.

In summary, by utilizing series of both enriched and population-basedcase series, we are optimizing the power to detect true associations,while at the same time gaining the added value of genotyping in awell-characterized population-based case control study.

Controls

Controls for both stages 1 and 2 will be women from EPIC study asdescribed above. The age distribution of the controls is similar to thatof the cases. Women who are known to have developed cancer, or who arenon-white, will be excluded. Controls for stage 1 will be sampled from asub cohort of 2,000 postmenopausal women for whom detailed analyses ofsex steroid hormones and mammographic density have been conducted²⁸.

Ethical approvals that cover the use of both case and control samplesfor genetic association studies have been obtained. Both cases andcontrols have given informed consent for their DNA to be used for suchgenetic studies.

Statistical Considerations Statistical Analysis

The primary analysis, at both stages 1 and 2, is to evaluate theassociation of each SNP individually with breast cancer. Epidemiologicalstudies suggest little or no difference in the relative risk of breastcancer between mothers of and sisters of cases, except possibly at veryyoung ages^(1,12), indicating that most susceptibility alleles havelittle recessive component (as in the polygenic model of Antoniou etal¹³). The primary analyses are, therefore, based on a trend test forthe difference in allele frequencies between cases and controls²⁹. Casesare weighted by family history to improve the efficiency of the test.

In principle, haplotype analysis or joint genotype analysis can providesome improvement in power³⁰. In the current design, however, haplotypeanalysis is largely redundant since only a small minority of SNPs willbe taken through to stage 2, and the power calculations have thereforeassumed single SNP analyses. The cost of taking all tagging SNPs in ablock through to stage 2 to allow full haplotype analyses would outweighany gain in power. Haplotype analysis is utilized in those cases wheremore than one linked SNP in the same LD block is typed at stage 2, andwill be utilized extensively in follow-up studies.

Power Calculations

The power of the study has been derived on the basis of a significancelevel of p=10⁻⁴ over both stages combined. Approximately 12 loci wouldbe expected to be significant at this level by chance (given the stageddesign), leaving a manageable number of loci to retest in larger seriesand a favourable ratio of “true”:“false” positives.

The power calculations assume that the cases in stage 1 have a familyhistory of two affected first degree relatives. In practice, the poweris somewhat greater since this is the minimum criterion and many of thecases will have a stronger family history. Examples of the power todetect a disease susceptibility allele are given in Table 2, fordifferent values of the disease allele frequency and relative risk,assuming the estimated distribution of r² from the tagging set. (Forpolymorphisms with alleles of frequency 0.05, the power has beencalculated by assuming that the polymorphism is in LD, at D′=1, with arandomly chosen common polymorphism from the set). For common alleles,the power is principally dependent on the contribution of the locus tothe overall genetic variance, and is at least 50% for loci explaining 1%of the variance and approximately 80% for loci explaining 2% of thevariance. In contrast, for alleles with frequency less than 5%, power ispoor unless the effect size is very large.

TABLE 2 Estimated overall power to detect a dominant susceptibilitylocus with a given allele frequency conferring a given relative risk (P< .0001 after two stages) assuming the distribution of r² between thesusceptibility locus and a tagging SNP based on previously reported data(Table 1). Percentage of overall genetic variance explained in brackets.Allele frequency Relative risk .2 .1 .05 1.2 53% (0.9%) 27% (0.6%) <1%(0.3%) 1.3 79% (2.0%) 61% (1.2%) <1% (0.7%) 1.5 91% (5.2%) 86% (3.2%) 6% (1.8%) 2.0 99% (17.8%)  97% (11.5%)  29% (6.7%)

For quantitative traits measured in the controls, the power isapproximately 50% to detect loci explaining at least 5% of thephenotypic variance, at the 5% significance level. These loci would beavailable for further evaluation in future large studies within the EPICcohort.

Detailed Evaluation of Susceptibility Loci

Once a significant association is identified, further polymorphisms areevaluated in the region in an attempt to establish the most stronglyassociated variant or haplotype. The general procedure will be similarto that used for investigating candidate genes. The available databasesare searched for known SNPs. Where no systematic search for allavailable SNPs has been conducted, in-house resequencing of a limitednumber of individuals (e.g., n=48) is used. After excluding SNPs thatare in complete LD, informative SNPs are genotyped in the cases andcontrols used in stages 1 and 2. Multiple logistic regression is used toinvestigate the joint effect of multiple SNPs. Further investigationscan be performed to identify functional variant(s).

Further Evaluation of Quantitative Trait Loci

SNPs that exhibit significant associations at stage 1 with quantitativetraits are available for replication in further series. Since the numberof quantitative traits is large, prioritization is performed on thebasis of the strength of the association, the plausibility of the locusand the importance of the phenotype. For example, associations withserum sex steroid hormone levels and mammographic density areprioritized favorably, because these are related to breast cancer risk.SNPs associated with these phenotypes are typed in a further 1,600samples from postmenopausal women in EPIC. If the associations arereplicated, they are pursued as above.

REFERENCES

-   1. Collaborative Group in Hormonal Factors in Breast Cancer (2001)    Familial breast cancer: collaborative reanalysis of individual data    from 52 epidemiological studies including 58,209 women with breast    cancer and 101,986 women without the disease. Lancet 358:1389-1399.-   2. Lichtenstein P et al (2000) Environmental and heritable factors    in the causation of cancer—analyses of cohorts of twins from Sweden,    Denmark, and Finland. New Engl J Med 243:78-85.-   3. Peto J, Mack T M (2000) High constant incidence in twins and    other relatives of women with breast cancer. Nature Genet    26:411-414.-   4. Antoniou A et al (2003) Average risks of breast and ovarian    cancer associated with mutations in BRCAJ or BRCA2 detected in case    series unselected for family history: a combined analysis of 22    studies. Am J Hum Genet 72:1117-1130.-   5. Peto J et. al (1989) The prevalence of BRCAJ and BRCA2 mutations    amongst early onset breast cancer cases in the U.K. J Natl Cancer    Inst 91:943-949.-   6. The Anglian Breast Cancer Study Group (2000) Prevalence of BRCA1    and BRCA2 mutations in a large population based series of breast    cancer cases. Br J Cancer 83:1301-1308.-   7. Easton D F (1999) How many more breast cancer predisposition    genes are there? Breast Cancer Res 1: 1-4.-   8. Ford D et al (1998) Genetic heterogeneity and Penetrance analysis    of the BRCA1 and BRCA2 genes in breast cancer families. Am J Hum    Genet 62:334-345.-   9. Thompson D et al (2002) Evaluation of linkage of breast cancer to    the putative BRCA3 locus on chromosome 13q21 in 128 multiple case    families from the Breast Cancer Linkage Consortium. Proc Natl Acad    Sci USA 99:827-831.-   10. Huusko P et al (2003) Genome-wide scanning for linkage in    Finnish breast cancer families. Eur J Hum Genet, in press.-   11. Antoniou A C et al (2001) Evidence for further breast cancer    susceptibility genes in addition to BRCA1 and BRCA2 in a population    based study. Genet Epidemiol 21: 1-18.-   12. Cui J et al (2000) After BRCA1 and BRCA2—what next?    Multifactorial segregation analysis of three-generational,    population-based Australian female breast cancer families. Am J Hum    Genet 68:420-431.-   13. Antoniou A C et al (2002) A comprehensive model for familial    breast cancer incorporating BRCA1, BRCA2 and other genes. Brit J    Cancer 86:76-83.-   14. Pharoah P D P et al (2002) Polygenic susceptibility to breast    cancer and implications for prevention. Nature Genetics 31:33-36.-   15. Titus-Emstoff L et al (1998) Menstrual factors in relation to    breast cancer risk. Cancer Epidemiol Biomarkers Prev. 7: 783-9.-   16. Kriege et al (2003) MRI screening for breast cancer in women    with high familial and genetic risk: First results of the Dutch MRI    screening study (MRISC). Proc Am Soc Clin Oncol 22:A5.-   17. Patil N et al (2001) Blocks of limited haplotype diversity    revealed by high-resolution scanning of human chromosome 21. Science    294:1719-1723.-   18. Zhang K et al (2002) A dynamic programming algorithm for    haplotype block partitioning. Proc Natl Acad Sci USA 99: 7335-7339.-   19. Pritchard J K, Przeworski M (2001) Linkage disequilibrium in    humans: models and data. Am J Hurn Genet 69: 1-14.-   20. Dunning A M et al (1999). A systematic review of genetic    polymorphisms and breast cancer risk. Cancer Epidemiol Biomarkers    Prevention 8:843-854.-   21. Healey C S et al (2000) A common variant in BRCA2 is associated    with both breast cancer risk and prenatal viability. Nature Genet    26:362-364.-   22. Kuschel B et al (2002) Variants in DNA double strand break    repair genes and breast cancer susceptibility. Hum Mol Genet    11:1399-1407.-   23. Dunning A M et al (2003) A TGF˜-1 signal peptide variant    increases secretion in vitro and is associated with increased    incidence of invasive breast cancer. Cancer Res 63:2610-15.-   24. Day N et al (1999) EPIC-Norfolk: study design and    characteristics of the cohort. European Prospective Investigation of    Cancer. Br J Cancer 80 Suppl 1:95-103.-   25. Goode E L et al (2001) Assessment of population stratification    in a large population based cohort. Genet Epidemiol 21:A126.-   26. Antoniou A, Easton D F (2003) Polygenic inheritance of breast    cancer: implications for design of association studies. Genet    Epidemiol 25: 190-202.-   27. Satagopan J M et al (2002) Two-staged designs for gene-disease    association studies. Biometrics 58: 163-170.-   28. Dunning A M et al (2004) Polymorphisms associated with    circulating sex hormone levels in post-menopausal women. J Natl    Cancer Inst, in press.-   29. Sasieni P D (1997) From genotypes to genes: doubling the sample    size. Biometrics 53:1253-1261.-   30. Chapman J P et al (2003) Detecting disease associations due to    linkage disequilibrium using haplotype tags: a class of tests and    the determinants of statistical power. Hum Hered 56: 18-31.

Example 2 Marker Polymorphisms Associated with Breast CancerPredisposition

SNPs identified as being associated with breast cancer risk(predisposition) are set forth in FIGS. 1 and 2. FIG. 1 provides thecurrently most preferred associations; FIG. 2 provides additionalassociations.

Sequences for given dbSNP rsID numbers (see, “REFSNP ID,” column 2 fromthe Figures) are found at: www.ncbi.nlm.nih.gov/SNP/. In FIGS. 1 and 2,the second column is labeled “REFSNP ID”. The values in this column areSNP identification numbers according to the dbSNP database establishedand maintained by NCBI of the US National Library of Medicine at the USNational Institute of Health. The NCBI dbSNP database is publiclyaccessible and considerable additional information can be easily viewedby searching the database using the rsID numbers provided in the Figuresby entering the number prefixed by “rs” in the database search windowand clicking on “Search.” The information provided can include, but isnot limited to, alleles at the SNP locus, flanking nucleotide sequences,and submission information.

The SNP ID column numbers (See, column 1, FIGS. 1 and 2) referencepublicly available Perlegen SNP identification numbers, which can beviewed with associated information at Perlegen(dot)com, using thecompany's available genome browser atgenome(dot)perlegen(dot)com/browser/index(dot)html, following theinstructions provided (Perlegen Sciences, Inc., Menlo Park, Calif.). Asnoted in the instructions provided, wild card characters (e.g., “*”symbols) can be added at the beginning of the SNP ID to identifypertinent information for all alleles of the SNP. This database alsolinks to the NCBI genomic database. In the figures, the first row oneach page is a header row with the column names. The columns are asfollows:

Header description of content SNP_ID Perlegen internal SNP identifier.REFSNP_ID The dbSNP RefSNP cluster ID (from NCBI) when available. Can benull. SUBSNP_ID The dbSNP submission ID for SNPs Perlegen submitted todbSNP. Can be null. ACCESSION_ID The accession number from NCBI Build 35of the contig to which the SNP aligns; may be null. POSITION Nucleotideposition in NCBI build 35 contig of the reference base in the alignment;may be null. ALLELE_1 The nucleotide code for allele 1 (Perlegen refallele). ALLELE_2 The nucleotide code for allele 2 (Perlegen altallele). Ptrend_weighted The trend score p-value of the association,weighted by degree of family history for each sample Gene_name NCBI genedatabase symbol of a gene near SNP geneDescription NCBI gene databasedescription of the gene HIT_TYPE The type of hit: exon, intron, up(within 10 kb upstream of transcription start site), down (within 10 kbdownstream of the transcription stop). Numbers indicate distancesgreater than 10 kb, in addition to hit type.

While the foregoing invention has been described in some detail forpurposes of clarity and understanding, it will be clear to one skilledin the art from a reading of this disclosure that various changes inform and detail can be made without departing from the true scope of theinvention. For example, all the techniques and apparatus described abovecan be used in various combinations. All publications, patents, patentapplications, and/or other documents cited in this application areincorporated by reference in their entirety for all purposes to the sameextent as if each individual publication, patent, patent application,and/or other document were individually indicated to be incorporated byreference for all purposes.

1. A method of identifying a human female subject as having a breastcancer susceptibility phenotype, the method comprising: detecting, in abiological sample derived from the human female subject, an inheritedpolymorphism, comprising single nucleotide A/G polymorphism SNP 1990126(rs13281615) or a single nucleotide polymorphism in linkagedisequilibrium therewith with an r² value of at least 0.8, andidentifying the human female subject as having said breast cancersusceptibility phenotype if said single nucleotide polymorphism SNP1990126 or said single nucleotide polymorphism in linkage disequilibriumtherewith is detected.
 2. The method of claim 1, wherein the detectingcomprises amplifying or sequencing the single nucleotide polymorphismand detecting the single nucleotide polymorphism or sequence thereof. 3.The method of claim 2, wherein the amplifying comprises: a) admixing anamplification primer or amplification primer pair with a nucleic acidtemplate isolated from the biological sample, wherein the primer orprimer pair is complementary or partially complementary to a regionproximal to or including said single nucleotide polymorphism SNP 1990126or said single nucleotide polymorphism in linkage disequilibriumtherewith, and is capable of initiating nucleic acid polymerization by apolymerase on the nucleic acid template; and b) extending the primer orprimer pair in a DNA polymerization reaction comprising a polymerase andthe template nucleic acid to generate an amplicon.
 4. The method ofclaim 2, wherein the single nucleotide polymorphism is detected by aprocess that includes one or more of: sequencing the single nucleotidepolymorphism in a genomic DNA isolated from the biological sample,hybridizing the single nucleotide polymorphism or an amplicon thereof toan array, digesting the single nucleotide polymorphism or an ampliconthereof with a restriction enzyme, or real-time PCR amplification of thesingle nucleotide polymorphism.
 5. The method of claim 2, comprisingpartially or fully sequencing the inherited polymorphism in a nucleicacid isolated from the biological sample.
 6. The method of claim 2,wherein the amplifying comprises performing a polymerase chain reaction(PCR), reverse transcriptase PCR (RT-PCR), or ligase chain reaction(LCR) using a nucleic acid isolated from the biological sample as atemplate in the PCR, RT-PCR, or LCR.